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Ale L, Gentleman R, Sonmez TF, Sarkar D, Endres C. nhanesA: achieving transparency and reproducibility in NHANES research. Database (Oxford) 2024; 2024:baae028. [PMID: 38625809 PMCID: PMC11020206 DOI: 10.1093/database/baae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/08/2024] [Accepted: 03/23/2024] [Indexed: 04/18/2024]
Abstract
The National Health and Nutrition Examination Survey provides comprehensive data on demographics, sociology, health and nutrition. Conducted in 2-year cycles since 1999, most of its data are publicly accessible, making it pivotal for research areas like studying social determinants of health or tracking trends in health metrics such as obesity or diabetes. Assembling the data and analyzing it presents a number of technical and analytic challenges. This paper introduces the nhanesA R package, which is designed to assist researchers in data retrieval and analysis and to enable the sharing and extension of prior research efforts. We believe that fostering community-driven activity in data reproducibility and sharing of analytic methods will greatly benefit the scientific community and propel scientific advancements. Database URL: https://github.com/cjendres1/nhanes.
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Affiliation(s)
- Laha Ale
- School of Computing and Artificial Intelligence, Southwest Jiaotong University, No. 999, Xian Rd, Pidu Dist., Chengdu, Sichuan 611756, China
| | - Robert Gentleman
- Center for Computational Biomedicine, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
| | | | - Deepayan Sarkar
- Theoretical Statistics and Mathematics Unit, Indian Statistical Institute, 7 SJSS Marg, New Delhi 110016, India
| | - Christopher Endres
- The Promenade Dance Studio, Inc., 2605 Lord Baltimore Drive, Windsor Mill, MD 21244, USA
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2
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Geistlinger L, Vargas R, Lee T, Pan J, Huttlin EL, Gentleman R. BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions. Bioinformatics 2023; 39:7043092. [PMID: 36794911 PMCID: PMC9978581 DOI: 10.1093/bioinformatics/btad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/14/2023] [Accepted: 02/15/2023] [Indexed: 02/17/2023] Open
Abstract
SUMMARY The BioPlex project has created two proteome scale, cell-line-specific protein-protein interaction (PPI) networks: the first in 293T cells, including 120k interactions among 15k proteins; and the second in HCT116 cells, including 70k interactions between 10k proteins. Here, we describe programmatic access to the BioPlex PPI networks and integration with related resources from within R and Python. Besides PPI networks for 293T and HCT116 cells, this includes access to CORUM protein complex data, PFAM protein domain data, PDB protein structures, and transcriptome and proteome data for the two cell lines. The implemented functionality serves as a basis for integrative downstream analysis of BioPlex PPI data with domain-specific R and Python packages, including efficient execution of maximum scoring sub-network analysis, protein domain-domain association analysis, mapping of PPIs onto 3D protein structures and analysis of BioPlex PPIs at the interface of transcriptomic and proteomic data. AVAILABILITY AND IMPLEMENTATION The BioPlex R package is available from Bioconductor (bioconductor.org/packages/BioPlex), and the BioPlex Python package is available from PyPI (pypi.org/project/bioplexpy). Applications and downstream analyses are available from GitHub (github.com/ccb-hms/BioPlexAnalysis).
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Affiliation(s)
| | | | - Tyrone Lee
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua Pan
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Gentleman
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA
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3
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Lawrence M, Gentleman R. VariantTools: an extensible framework for developing and testing variant callers. Bioinformatics 2018; 33:3311-3313. [PMID: 29028267 PMCID: PMC5860039 DOI: 10.1093/bioinformatics/btx450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 07/11/2017] [Indexed: 11/12/2022] Open
Abstract
Motivation Variant calling is the complex task of separating real polymorphisms from errors. The appropriate strategy will depend on characteristics of the sample, the sequencing methodology and on the questions of interest. Results We present VariantTools, an extensible framework for developing and testing variant callers. There are facilities for reproducibly tallying, filtering, flagging and annotating variants. The tools are extensible, modular and flexible, so that they are tunable to particular use cases, and they interoperate with existing analysis software so that they can be embedded in established work flows. Availability and implementation VariantTools is available from http://www.bioconductor.org/. Contact michafla@gene.com. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michael Lawrence
- Department of Bioinformatics, Genentech, South San Francisco, CA, USA
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4
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Deverka PA, Majumder MA, Villanueva AG, Anderson M, Bakker AC, Bardill J, Boerwinkle E, Bubela T, Evans BJ, Garrison NA, Gibbs RA, Gentleman R, Glazer D, Goldstein MM, Greely H, Harris C, Knoppers BM, Koenig BA, Kohane IS, La Rosa S, Mattison J, O'Donnell CJ, Rai AK, Rehm HL, Rodriguez LL, Shelton R, Simoncelli T, Terry SF, Watson MS, Wilbanks J, Cook-Deegan R, McGuire AL. Creating a data resource: what will it take to build a medical information commons? Genome Med 2017; 9:84. [PMID: 28938910 PMCID: PMC5610432 DOI: 10.1186/s13073-017-0476-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
National and international public-private partnerships, consortia, and government initiatives are underway to collect and share genomic, personal, and healthcare data on a massive scale. Ideally, these efforts will contribute to the creation of a medical information commons (MIC), a comprehensive data resource that is widely available for both research and clinical uses. Stakeholder participation is essential in clarifying goals, deepening understanding of areas of complexity, and addressing long-standing policy concerns such as privacy and security and data ownership. This article describes eight core principles proposed by a diverse group of expert stakeholders to guide the formation of a successful, sustainable MIC. These principles promote formation of an ethically sound, inclusive, participant-centric MIC and provide a framework for advancing the policy response to data-sharing opportunities and challenges.
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Affiliation(s)
- Patricia A Deverka
- American Institutes for Research, Health Care Group, 100 Europa Drive, Suite 315, Chapel Hill, NC, 27517, USA
| | - Mary A Majumder
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Angela G Villanueva
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | - Annette C Bakker
- Children's Tumor Foundation, 120 Wall Street, 16th Floor, New York, NY, 10005, USA
| | - Jessica Bardill
- Department of English, Concordia University, 1455 Boulevard de Maisonneuve O, Montreal, QC, H3G 1M8, Canada
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Tania Bubela
- Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Barbara J Evans
- Law Center and Department of Electrical and Computer Engineering, University of Houston, 4604 Calhoun Road, Houston, TX, 77004, USA
| | - Nanibaa' A Garrison
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institutes, 1900 Ninth Avenue, Room 677, Seattle, WA, 98101, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | - David Glazer
- Verily Life Sciences LLC, 269 E. Grand Avenue, South San Francisco, CA, 94080, USA
| | - Melissa M Goldstein
- Milken Institute School of Public Health, The Georgetown Washington University, 950 New Hampshire Avenue, NW, Second Floor, Washington, DC, 20052, USA
| | - Hank Greely
- Center for Law and the Biosciences, Stanford University, Neukom N361, Stanford, CA, 94305, USA
| | - Crane Harris
- Illumina, Inc., 5200 Research Pl, San Diego, CA, 92122, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, 740 Avenue Drive Penfield, Suite 5200, Montreal, Quebec, H3A 0G1, Canada
| | - Barbara A Koenig
- Institute for Health and Aging, and Department of Anthropology, History, and Social Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA, 02115, USA
| | - Salvatore La Rosa
- Children's Tumor Foundation, 120 Wall Street, 16th Floor, New York, NY, 10005, USA
| | - John Mattison
- Kaiser Permanente, University of California San Diego and Singularity University, 4965 Maynard Street, San Diego, CA, 92122, USA
| | - Christopher J O'Donnell
- Center for Population Genomics, Boston Veterans Administration Healthcare, 73 Mount Wayte Avenue, Framingham, MA, 01702, USA
| | - Arti K Rai
- Duke University School of Law; Duke Innovation and Entrepreneurship Initiative, 210 Science Drive, Box 90360, Durham, NC, 27708, USA
| | - Heidi L Rehm
- Harvard Medical School, Brigham and Women's Hospital and The Broad Institute of MIT and Harvard, 65 Landsdowne Street, Cambridge, MA, 02139, USA
| | - Laura L Rodriguez
- Division of Policy, Communications, and Education, National Human Genome Research Institute 31 Center Drive, Room 4B09, Bethesda, MD, 20892, USA
| | - Robert Shelton
- Private Access, Inc, 19800 MacArthur Boulevard, Suite 300, Irvine, CA, 92612, USA
| | - Tania Simoncelli
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - Sharon F Terry
- Genetic Alliance, 4301 Connecticut Avenue, NW, Suite 404, Washington, DC, 20008, USA
| | - Michael S Watson
- American College of Medical Genetics and Genomics, 7101 Wisconsin Avenue, Suite 1101, Bethesda, MD, 20814, USA
| | - John Wilbanks
- Sage Bionetworks, 1100 Fairview Avenue N., Mailstop M1-C108, Seattle, WA, 98109, USA
| | - Robert Cook-Deegan
- School for the Future of Innovation in Society and Consortium for Science, Policy and Outcomes, Arizona State University, and Senior Fellow, FasterCures, a Center of the Milken Institute, 1834 Connecticut Avenue, NW, Washington, DC, 20009, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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Becker G, Barr C, Gentleman R, Lawrence M. Enhancing Reproducibility and Collaboration via Management of R Package Cohorts. J Stat Softw 2017. [DOI: 10.18637/jss.v082.i01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Goldstein LD, Lee J, Gnad F, Klijn C, Schaub A, Reeder J, Daemen A, Bakalarski CE, Holcomb T, Shames DS, Hartmaier RJ, Chmielecki J, Seshagiri S, Gentleman R, Stokoe D. Recurrent Loss of NFE2L2 Exon 2 Is a Mechanism for Nrf2 Pathway Activation in Human Cancers. Cell Rep 2016; 16:2605-2617. [PMID: 27568559 DOI: 10.1016/j.celrep.2016.08.010] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 06/03/2016] [Accepted: 07/31/2016] [Indexed: 12/21/2022] Open
Abstract
The Nrf2 pathway is frequently activated in human cancers through mutations in Nrf2 or its negative regulator KEAP1. Using a cell-line-derived gene signature for Nrf2 pathway activation, we found that some tumors show high Nrf2 activity in the absence of known mutations in the pathway. An analysis of splice variants in oncogenes revealed that such tumors express abnormal transcript variants from the NFE2L2 gene (encoding Nrf2) that lack exon 2, or exons 2 and 3, and encode Nrf2 protein isoforms missing the KEAP1 interaction domain. The Nrf2 alterations result in the loss of interaction with KEAP1, Nrf2 stabilization, induction of a Nrf2 transcriptional response, and Nrf2 pathway dependence. In all analyzed cases, transcript variants were the result of heterozygous genomic microdeletions. Thus, we identify an alternative mechanism for Nrf2 pathway activation in human tumors and elucidate its functional consequences.
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Affiliation(s)
- Leonard D Goldstein
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080, USA; Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - James Lee
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Florian Gnad
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Christiaan Klijn
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Annalisa Schaub
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Jens Reeder
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Anneleen Daemen
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Corey E Bakalarski
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA; Department of Protein Chemistry, Genentech Inc., South San Francisco, CA 94080, USA
| | - Thomas Holcomb
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - David S Shames
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | | | | | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Robert Gentleman
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - David Stokoe
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA 94080, USA.
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Goldstein LD, Cao Y, Pau G, Lawrence M, Wu TD, Seshagiri S, Gentleman R. Prediction and Quantification of Splice Events from RNA-Seq Data. PLoS One 2016; 11:e0156132. [PMID: 27218464 PMCID: PMC4878813 DOI: 10.1371/journal.pone.0156132] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 04/18/2016] [Indexed: 01/24/2023] Open
Abstract
Analysis of splice variants from short read RNA-seq data remains a challenging problem. Here we present a novel method for the genome-guided prediction and quantification of splice events from RNA-seq data, which enables the analysis of unannotated and complex splice events. Splice junctions and exons are predicted from reads mapped to a reference genome and are assembled into a genome-wide splice graph. Splice events are identified recursively from the graph and are quantified locally based on reads extending across the start or end of each splice variant. We assess prediction accuracy based on simulated and real RNA-seq data, and illustrate how different read aligners (GSNAP, HISAT2, STAR, TopHat2) affect prediction results. We validate our approach for quantification based on simulated data, and compare local estimates of relative splice variant usage with those from other methods (MISO, Cufflinks) based on simulated and real RNA-seq data. In a proof-of-concept study of splice variants in 16 normal human tissues (Illumina Body Map 2.0) we identify 249 internal exons that belong to known genes but are not related to annotated exons. Using independent RNA samples from 14 matched normal human tissues, we validate 9/9 of these exons by RT-PCR and 216/249 by paired-end RNA-seq (2 x 250 bp). These results indicate that de novo prediction of splice variants remains beneficial even in well-studied systems. An implementation of our method is freely available as an R/Bioconductor package SGSeq.
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Affiliation(s)
- Leonard D. Goldstein
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA, United States of America
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, United States of America
- * E-mail:
| | - Yi Cao
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA, United States of America
| | - Gregoire Pau
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA, United States of America
| | - Michael Lawrence
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA, United States of America
| | - Thomas D. Wu
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA, United States of America
| | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, United States of America
| | - Robert Gentleman
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA, United States of America
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8
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Huntley MA, Lou M, Goldstein LD, Lawrence M, Dijkgraaf GJP, Kaminker JS, Gentleman R. Complex regulation of ADAR-mediated RNA-editing across tissues. BMC Genomics 2016; 17:61. [PMID: 26768488 PMCID: PMC4714477 DOI: 10.1186/s12864-015-2291-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/11/2015] [Indexed: 01/28/2023] Open
Abstract
Background RNA-editing is a tightly regulated, and essential cellular process for a properly functioning brain. Dysfunction of A-to-I RNA editing can have catastrophic effects, particularly in the central nervous system. Thus, understanding how the process of RNA-editing is regulated has important implications for human health. However, at present, very little is known about the regulation of editing across tissues, and individuals. Results Here we present an analysis of RNA-editing patterns from 9 different tissues harvested from a single mouse. For comparison, we also analyzed data for 5 of these tissues harvested from 15 additional animals. We find that tissue specificity of editing largely reflects differential expression of substrate transcripts across tissues. We identified a surprising enrichment of editing in intronic regions of brain transcripts, that could account for previously reported higher levels of editing in brain. There exists a small but remarkable amount of editing which is tissue-specific, despite comparable expression levels of the edit site across multiple tissues. Expression levels of editing enzymes and their isoforms can explain some, but not all of this variation. Conclusions Together, these data suggest a complex regulation of the RNA-editing process beyond transcript expression levels. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2291-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melanie A Huntley
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Melanie Lou
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Leonard D Goldstein
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Michael Lawrence
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Gerrit J P Dijkgraaf
- Department of Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Joshua S Kaminker
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
| | - Robert Gentleman
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, USA.
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Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. Erratum: The anatomy of successful computational biology software. Nat Biotechnol 2014. [DOI: 10.1038/nbt0614-592b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ. Software for computing and annotating genomic ranges. PLoS Comput Biol 2013; 9:e1003118. [PMID: 23950696 PMCID: PMC3738458 DOI: 10.1371/journal.pcbi.1003118] [Citation(s) in RCA: 2329] [Impact Index Per Article: 211.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 05/07/2013] [Indexed: 11/23/2022] Open
Abstract
We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.
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Affiliation(s)
- Michael Lawrence
- Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, California, United States of America.
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12
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13
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14
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Abstract
R is a powerful language and widely used software tool for the analysis and visualization of data. Its core capabilities can be extended through many different add-on packages. Among the many packages are some which offer a broad range of facilities for analyzing statistical properties of graphs. This chapter provides a practical tutorial covering the use of R methods for graphs and networks to examine biological data and analyze their topological and statistical properties.
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Affiliation(s)
- Nolwenn Le Meur
- IRISA, Equipe Symbiose, Université de Rennes I, Rennes, France.
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15
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Knouf EC, Garg K, Arroyo JD, Correa Y, Sarkar D, Parkin RK, Wurz K, O'Briant KC, Godwin AK, Urban ND, Ruzzo WL, Gentleman R, Drescher CW, Swisher EM, Tewari M. An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription. Nucleic Acids Res 2011; 40:499-510. [PMID: 21917857 PMCID: PMC3258134 DOI: 10.1093/nar/gkr731] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although microRNAs (miRNAs) are important regulators of gene expression, the transcriptional regulation of miRNAs themselves is not well understood. We employed an integrative computational pipeline to dissect the transcription factors (TFs) responsible for altered miRNA expression in ovarian carcinoma. Using experimental data and computational predictions to define miRNA promoters across the human genome, we identified TFs with binding sites significantly overrepresented among miRNA genes overexpressed in ovarian carcinoma. This pipeline nominated TFs of the p53/p63/p73 family as candidate drivers of miRNA overexpression. Analysis of data from an independent set of 253 ovarian carcinomas in The Cancer Genome Atlas showed that p73 and p63 expression is significantly correlated with expression of miRNAs whose promoters contain p53/p63/p73 family binding sites. In experimental validation of specific miRNAs predicted by the analysis to be regulated by p73 and p63, we found that p53/p63/p73 family binding sites modulate promoter activity of miRNAs of the miR-200 family, which are known regulators of cancer stem cells and epithelial–mesenchymal transitions. Furthermore, in chromatin immunoprecipitation studies both p73 and p63 directly associated with the miR-200b/a/429 promoter. This study delineates an integrative approach that can be applied to discover transcriptional regulatory mechanisms in other biological settings where analogous genomic data are available.
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Affiliation(s)
- Emily C Knouf
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C. Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) 2011; 2011:baq027. [PMID: 21205783 PMCID: PMC3017395 DOI: 10.1093/database/baq027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases.
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Affiliation(s)
- Pascale Gaudet
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- *Corresponding author: Tel: +41-22-379-5050; Fax: +41-22-379-5858;
| | - Amos Bairoch
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Dawn Field
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Susanna-Assunta Sansone
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chris Taylor
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Teresa K. Attwood
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alex Bateman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Judith A. Blake
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carol J. Bult
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - J. Michael Cherry
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Rex L. Chisholm
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Guy Cochrane
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Charles E. Cook
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Janan T. Eppig
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael Y. Galperin
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robert Gentleman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carole A. Goble
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Takashi Gojobori
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - John M. Hancock
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Douglas G. Howe
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tadashi Imanishi
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Janet Kelso
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - David Landsman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Suzanna E. Lewis
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ilene Karsch Mizrachi
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sandra Orchard
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - B.F. Francis Ouellette
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Shoba Ranganathan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Lorna Richardson
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Philippe Rocca-Serra
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Paul N. Schofield
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Damian Smedley
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Christopher Southan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tin W. Tan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tatiana Tatusova
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Patricia L. Whetzel
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Owen White
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chisato Yamasaki
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR UK, University of Oxford, Oxford e-Research Centre, Oxford, OX1 3QG, UK, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, School of Computer Science, The University of Manchester, Manchester M13 9PT, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA, Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, USA, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Japan, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, CA 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK, Dept of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA 94305, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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17
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Ochs MF, Karchin R, Ressom H, Gentleman R. Identification of aberrant pathway and network activity from high-throughput data. Pac Symp Biocomput 2011:364-368. [PMID: 21121064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The workshop focused on approaches to deduce changes in biological activity in cellular pathways and networks that drive phenotype from high-throughput data. Work in cancer has demonstrated conclusively that cancer etiology is driven not by single gene mutation or expression change, but by coordinated changes in multiple signaling pathways. These pathway changes involve different genes in different individuals, leading to the failure of gene-focused analysis to identify the full range of mutations or expression changes driving cancer development. There is also evidence that metabolic pathways rather than individual genes play the critical role in a number of metabolic diseases. Tools to look at pathways and networks are needed to improve our understanding of disease and to improve our ability to target therapeutics at appropriate points in these pathways.
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Affiliation(s)
- M F Ochs
- Departments of Oncology and Health Science Informatics, Johns Hopkins University, Baltimore, MD 19075, USA.
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18
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Palii CG, Perez-Iratxeta C, Yao Z, Cao Y, Dai F, Davison J, Atkins H, Allan D, Dilworth FJ, Gentleman R, Tapscott SJ, Brand M. Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages. EMBO J 2010; 30:494-509. [PMID: 21179004 PMCID: PMC3034015 DOI: 10.1038/emboj.2010.342] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 11/30/2010] [Indexed: 12/03/2022] Open
Abstract
Expression of the basic helix-loop-helix transcription factor TAL1/SCL is required for erythrocyte differentiation; aberrant expression in lymphoid cells leads to oncogenic transformation. Here, global analysis of TAL1 binding in erythroid and malignant T cells identifies cell type specific functional interaction with the transcription factors RUNX and ETS1. TAL1/SCL is a master regulator of haematopoiesis whose expression promotes opposite outcomes depending on the cell type: differentiation in the erythroid lineage or oncogenesis in the T-cell lineage. Here, we used a combination of ChIP sequencing and gene expression profiling to compare the function of TAL1 in normal erythroid and leukaemic T cells. Analysis of the genome-wide binding properties of TAL1 in these two haematopoietic lineages revealed new insight into the mechanism by which transcription factors select their binding sites in alternate lineages. Our study shows limited overlap in the TAL1-binding profile between the two cell types with an unexpected preference for ETS and RUNX motifs adjacent to E-boxes in the T-cell lineage. Furthermore, we show that TAL1 interacts with RUNX1 and ETS1, and that these transcription factors are critically required for TAL1 binding to genes that modulate T-cell differentiation. Thus, our findings highlight a critical role of the cellular environment in modulating transcription factor binding, and provide insight into the mechanism by which TAL1 inhibits differentiation leading to oncogenesis in the T-cell lineage.
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Affiliation(s)
- Carmen G Palii
- The Sprott Center for Stem Cell Research, Department of Regenerative Medicine, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
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19
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Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BFF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res 2010; 39:D7-10. [PMID: 21097465 PMCID: PMC3013734 DOI: 10.1093/nar/gkq1173] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases.
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Affiliation(s)
- Pascale Gaudet
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- *To whom correspondence should be addressed. Tel: +41 22 379 5050; Fax: +41 22 379 5858;
| | - Amos Bairoch
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Dawn Field
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Susanna-Assunta Sansone
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chris Taylor
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Teresa K. Attwood
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alex Bateman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Judith A. Blake
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carol J. Bult
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - J. Michael Cherry
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Rex L. Chisholm
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Guy Cochrane
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Charles E. Cook
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Janan T. Eppig
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael Y. Galperin
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robert Gentleman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carole A. Goble
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Takashi Gojobori
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - John M. Hancock
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Douglas G. Howe
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tadashi Imanishi
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Janet Kelso
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - David Landsman
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Suzanna E. Lewis
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ilene Karsch Mizrachi
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sandra Orchard
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - B. F. Francis Ouellette
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Shoba Ranganathan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Lorna Richardson
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Philippe Rocca-Serra
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Paul N. Schofield
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Damian Smedley
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Christopher Southan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tin Wee Tan
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tatiana Tatusova
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Patricia L. Whetzel
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Owen White
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chisato Yamasaki
- Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA, NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, School of Computer Science, The University of Manchester, Manchester M13 9PT, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, Department of Genetics, Stanford University, Stanford, California 94305-5120, NCBI, NLM, National Institutes of Health, Bethesda, MD 20894, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA, DATABASE, The Journal of Biological Databases and Curation, Oxford University Press, Oxford OX2 6DP, UK, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi Koto-ku, Tokyo 135-0064, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan, MRC Harwell, Mammalian Genetics Unit, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK, The Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, Oregon 97401-5291, USA, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road 64R0121 Berkeley, California 94720, USA, Ontario Institute for Cancer Research, Suite 800, 101 College Street, Toronto, Ontario, M5G 0A3, Canada, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, Department of Physiology, Development and Neuroscience, University of Cambridge, Doning Street, Cambridge CB2 3EG, UK, ChrisDS Consulting, Göteborg, Sweden, Stanford Center for Biomedical Informatics Research, National Center for Biomedical Ontology, Stanford University, Stanford, CA, 94305 and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Hahne F, Khodabakhshi AH, Bashashati A, Wong CJ, Gascoyne RD, Weng AP, Seyfert-Margolis V, Bourcier K, Asare A, Lumley T, Gentleman R, Brinkman RR. Per-channel basis normalization methods for flow cytometry data. Cytometry A 2010; 77:121-31. [PMID: 19899135 DOI: 10.1002/cyto.a.20823] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Between-sample variation in high-throughput flow cytometry data poses a significant challenge for analysis of large-scale data sets, such as those derived from multicenter clinical trials. It is often hard to match biologically relevant cell populations across samples because of technical variation in sample acquisition and instrumentation differences. Thus, normalization of data is a critical step before analysis, particularly in large-scale data sets from clinical trials, where group-specific differences may be subtle and patient-to-patient variation common. We have developed two normalization methods that remove technical between-sample variation by aligning prominent features (landmarks) in the raw data on a per-channel basis. These algorithms were tested on two independent flow cytometry data sets by comparing manually gated data, either individually for each sample or using static gating templates, before and after normalization. Our results show a marked improvement in the overlap between manual and static gating when the data are normalized, thereby facilitating the use of automated analyses on large flow cytometry data sets. Such automated analyses are essential for high-throughput flow cytometry.
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Affiliation(s)
- Florian Hahne
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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21
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Bankhead A, Sach I, Ni C, LeMeur N, Kruger M, Ferrer M, Gentleman R, Rohl C. Knowledge based identification of essential signaling from genome-scale siRNA experiments. BMC Syst Biol 2009; 3:80. [PMID: 19653913 PMCID: PMC2731733 DOI: 10.1186/1752-0509-3-80] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 08/05/2009] [Indexed: 11/10/2022]
Abstract
Background A systems biology interpretation of genome-scale RNA interference (RNAi) experiments is complicated by scope, experimental variability and network signaling robustness. Over representation approaches (ORA), such as the Hypergeometric or z-score, are an established statistical framework used to associate RNA interference effectors to biologically annotated gene sets or pathways. These methods, however, do not directly take advantage of our growing understanding of the interactome. Furthermore, these methods can miss partial pathway activation and may be biased by protein complexes. Here we present a novel ORA, protein interaction permutation analysis (PIPA), that takes advantage of canonical pathways and established protein interactions to identify pathways enriched for protein interactions connecting RNAi hits. Results We use PIPA to analyze genome-scale siRNA cell growth screens performed in HeLa and TOV cell lines. First we show that interacting gene pair siRNA hits are more reproducible than single gene hits. Using protein interactions, PIPA identifies enriched pathways not found using the standard Hypergeometric analysis including the FAK cytoskeletal remodeling pathway. Different branches of the FAK pathway are distinctly essential in HeLa versus TOV cell lines while other portions are uneffected by siRNA perturbations. Enriched hits belong to protein interactions associated with cell cycle regulation, anti-apoptosis, and signal transduction. Conclusion PIPA provides an analytical framework to interpret siRNA screen data by merging biologically annotated gene sets with the human interactome. As a result we identify pathways and signaling hypotheses that are statistically enriched to effect cell growth in human cell lines. This method provides a complementary approach to standard gene set enrichment that utilizes the additional knowledge of specific interactions within biological gene sets.
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Affiliation(s)
- Armand Bankhead
- Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck & Co,, Inc, Seattle, WA 98109, USA.
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22
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Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 2009; 25:2607-8. [PMID: 19654119 PMCID: PMC2752612 DOI: 10.1093/bioinformatics/btp450] [Citation(s) in RCA: 362] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Summary:ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources. Availability and Implementation: This package is implemented in R and available at the Bioconductor web site; the package contains a ‘vignette’ outlining typical work flows. Contact:mtmorgan@fhcrc.org
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Affiliation(s)
- Martin Morgan
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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23
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Abstract
Summary: The rtracklayer package supports the integration of existing genome browsers with experimental data analyses performed in R. The user may (i) transfer annotation tracks to and from a genome browser and (ii) create and manipulate browser views to focus on a particular set of annotations in a specific genomic region. Currently, the UCSC genome browser is supported. Availability: The package is freely available from http://www.bioconductor.org/. A quick-start vignette is included with the package. Contact:mflawren@fhcrc.org
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Affiliation(s)
- Michael Lawrence
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA.
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Hahne F, LeMeur N, Brinkman RR, Ellis B, Haaland P, Sarkar D, Spidlen J, Strain E, Gentleman R. flowCore: a Bioconductor package for high throughput flow cytometry. BMC Bioinformatics 2009; 10:106. [PMID: 19358741 PMCID: PMC2684747 DOI: 10.1186/1471-2105-10-106] [Citation(s) in RCA: 349] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 04/09/2009] [Indexed: 11/28/2022] Open
Abstract
Background Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or drug discovery settings. However, data management and data analysis methods have not advanced sufficiently far from the initial small-scale studies to support modeling in the presence of multiple covariates. Results We developed a set of flexible open source computational tools in the R package flowCore to facilitate the analysis of these complex data. A key component of which is having suitable data structures that support the application of similar operations to a collection of samples or a clinical cohort. In addition, our software constitutes a shared and extensible research platform that enables collaboration between bioinformaticians, computer scientists, statisticians, biologists and clinicians. This platform will foster the development of novel analytic methods for flow cytometry. Conclusion The software has been applied in the analysis of various data sets and its data structures have proven to be highly efficient in capturing and organizing the analytic work flow. Finally, a number of additional Bioconductor packages successfully build on the infrastructure provided by flowCore, open new avenues for flow data analysis.
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Affiliation(s)
- Florian Hahne
- Life Sciences Department, Computational Biology Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.
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Carey VJ, Davis AR, Lawrence MF, Gentleman R, Raby BA. Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x. Bioinformatics 2009; 25:1447-8. [PMID: 19349284 DOI: 10.1093/bioinformatics/btp169] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R/Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware. AVAILABILITY AND IMPLEMENTATION Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at (http://www.bioconductor.org).
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Affiliation(s)
- Vincent J Carey
- Channing Laboratory, Department of Medicine, I2B2 National Center for Biocomputing, Brigham and Women's Hospital, Boston, MA 02115, USA.
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26
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Affiliation(s)
- David Landsman
- Potomac, MD, USA, Seattle, WA, USA, Leipzig, Germany and Toronto, ON, Canada
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Carey VJ, Gentleman R. Interpreting genetics of gene expression: integrative architecture in Bioconductor. Pac Symp Biocomput 2009:380-90. [PMID: 19209716 PMCID: PMC3378382 DOI: 10.1142/9789812836939_0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Several influential studies of genotypic determinants of gene expression in humans have now been published based on various populations including HapMap cohorts. The magnitude of the analytic task (transcriptome vs. SNP-genome) is a hindrance to dissemination of efficient, thorough, and auditable inference methods for this project. We describe the structure and use of Bioconductor facilities for inference in genetics of gene expression, with simultaneous application to multiple HapMap cohorts. Tools distributed for this purpose are readily adapted for the structure and analysis of privately-generated data in expression genetics.
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Affiliation(s)
- V J Carey
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Ave., Boston, MA 02115, USA.
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28
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Abstract
SUMMARY The assessment of data quality is a major concern in microarray analysis. arrayQualityMetrics is a Bioconductor package that provides a report with diagnostic plots for one or two colour microarray data. The quality metrics assess reproducibility, identify apparent outlier arrays and compute measures of signal-to-noise ratio. The tool handles most current microarray technologies and is amenable to use in automated analysis pipelines or for automatic report generation, as well as for use by individuals. The diagnosis of quality remains, in principle, a context-dependent judgement, but our tool provides powerful, automated, objective and comprehensive instruments on which to base a decision. AVAILABILITY arrayQualityMetrics is a free and open source package, under LGPL license, available from the Bioconductor project at www.bioconductor.org. A users guide and examples are provided with the package. Some examples of HTML reports generated by arrayQualityMetrics can be found at http://www.microarray-quality.org
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Affiliation(s)
- Audrey Kauffmann
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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29
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Sarkar D, Parkin R, Wyman S, Bendoraite A, Sather C, Delrow J, Godwin AK, Drescher C, Huber W, Gentleman R, Tewari M. Quality assessment and data analysis for microRNA expression arrays. Nucleic Acids Res 2008; 37:e17. [PMID: 19103660 PMCID: PMC2632898 DOI: 10.1093/nar/gkn932] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MicroRNAs are small (approximately 22 nt) RNAs that regulate gene expression and play important roles in both normal and disease physiology. The use of microarrays for global characterization of microRNA expression is becoming increasingly popular and has the potential to be a widely used and valuable research tool. However, microarray profiling of microRNA expression raises a number of data analytic challenges that must be addressed in order to obtain reliable results. We introduce here a universal reference microRNA reagent set as well as a series of nonhuman spiked-in synthetic microRNA controls, and demonstrate their use for quality control and between-array normalization of microRNA expression data. We also introduce diagnostic plots designed to assess and compare various normalization methods. We anticipate that the reagents and analytic approach presented here will be useful for improving the reliability of microRNA microarray experiments.
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Affiliation(s)
- D Sarkar
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA.
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30
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Affiliation(s)
- Robert Gentleman
- Department of Biostatistical Science; Dana Färber Cancer Insitute Harvard University; Boston, MA 02115 USA
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31
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Abstract
BACKGROUND Synthetic lethality defines a genetic interaction where the combination of mutations in two or more genes leads to cell death. The implications of synthetic lethal screens have been discussed in the context of drug development as synthetic lethal pairs could be used to selectively kill cancer cells, but leave normal cells relatively unharmed. A challenge is to assess genome-wide experimental data and integrate the results to better understand the underlying biological processes. We propose statistical and computational tools that can be used to find relationships between synthetic lethality and cellular organizational units. RESULTS In Saccharomyces cerevisiae, we identified multi-protein complexes and pairs of multi-protein complexes that share an unusually high number of synthetic genetic interactions. As previously predicted, we found that synthetic lethality can arise from subunits of an essential multi-protein complex or between pairs of multi-protein complexes. Finally, using multi-protein complexes allowed us to take into account the pleiotropic nature of the gene products. CONCLUSIONS Modeling synthetic lethality using current estimates of the yeast interactome is an efficient approach to disentangle some of the complex molecular interactions that drive a cell. Our model in conjunction with applied statistical methods and computational methods provides new tools to better characterize synthetic genetic interactions.
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Affiliation(s)
- Nolwenn Le Meur
- Division of Public Health Sciences, Fred Hutchinson Cancer Center Research, Program in Computational Biology, Seattle, WA 98109, USA.
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32
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Abstract
MOTIVATION Gene-set enrichment analysis (GSEA) can be greatly enhanced by linear model (regression) diagnostic techniques. Diagnostics can be used to identify outlying or influential samples, and also to evaluate model fit and explore model expansion. RESULTS We demonstrate this methodology on an adult acute lymphoblastic leukemia (ALL) dataset, using GSEA based on chromosome-band mapping of genes. Individual residuals, grouped or aggregated by chromosomal loci, indicate problematic samples and potential data-entry errors, and help identify hyperdiploidy as a factor playing a key role in expression for this dataset. Subsequent analysis pinpoints suspected DNA copy number abnormalities of specific samples and chromosomes (most prevalent are chromosomes X, 21 and 14), and also reveals significant expression differences between the hyperdiploid and diploid groups on other chromosomes (most prominently 19, 22, 3 and 13)--differences which are apparently not associated with copy number. AVAILABILITY Software for the statistical tools demonstrated in this article is available as Bioconductor package GSEAlm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Assaf P Oron
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.
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33
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Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R, Ruohola-Baker H, Tewari M. MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells 2008; 26:2496-505. [PMID: 18583537 DOI: 10.1634/stemcells.2008-0356] [Citation(s) in RCA: 234] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We used massively parallel pyrosequencing to discover and characterize microRNAs (miRNAs) expressed in human embryonic stem cells (hESC). Sequencing of small RNA cDNA libraries derived from undifferentiated hESC and from isogenic differentiating cultures yielded a total of 425,505 high-quality sequence reads. A custom data analysis pipeline delineated expression profiles for 191 previously annotated miRNAs, 13 novel miRNAs, and 56 candidate miRNAs. Further characterization of a subset of the novel miRNAs in Dicer-knockdown hESC demonstrated Dicer-dependent expression, providing additional validation of our results. A set of 14 miRNAs (9 known and 5 novel) was noted to be expressed in undifferentiated hESC and then strongly downregulated with differentiation. Functional annotation analysis of predicted targets of these miRNAs and comparison with a null model using non-hESC-expressed miRNAs identified statistically enriched functional categories, including chromatin remodeling and lineage-specific differentiation annotations. Finally, integration of our data with genome-wide chromatin immunoprecipitation data on OCT4, SOX2, and NANOG binding sites implicates these transcription factors in the regulation of nine of the novel/candidate miRNAs identified here. Comparison of our results with those of recent deep sequencing studies in mouse and human ESC shows that most of the novel/candidate miRNAs found here were not identified in the other studies. The data indicate that hESC express a larger complement of miRNAs than previously appreciated, and they provide a resource for additional studies of miRNA regulation of hESC physiology. Disclosure of potential conflicts of interest is found at the end of this article.
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Affiliation(s)
- Merav Bar
- Divisions of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Chiang T, Scholtens D, Sarkar D, Gentleman R, Huber W. Coverage and error models of protein-protein interaction data by directed graph analysis. Genome Biol 2008; 8:R186. [PMID: 17845715 PMCID: PMC2375024 DOI: 10.1186/gb-2007-8-9-r186] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 05/26/2007] [Accepted: 09/10/2007] [Indexed: 01/10/2023] Open
Abstract
Using a directed graph model for bait to prey systems and a multinomial error model, we assessed the error statistics in all published large-scale datasets for Saccharomyces cerevisiae and characterized them by three traits: the set of tested interactions, artifacts that lead to false-positive or false-negative observations, and estimates of the stochastic error rates that affect the data. These traits provide a prerequisite for the estimation of the protein interactome and its modules.
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Affiliation(s)
- Tony Chiang
- EMBL, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Fred Hutchinson Cancer Research Center, Computational Biology Group, Fairview Avenue North, Seattle, WA 98109-1024, USA
| | - Denise Scholtens
- Northwestern University, Department of Preventive Medicine, N Lake Shore Drive, Chicago, IL 60611-4402, USA
| | - Deepayan Sarkar
- Fred Hutchinson Cancer Research Center, Computational Biology Group, Fairview Avenue North, Seattle, WA 98109-1024, USA
| | - Robert Gentleman
- Fred Hutchinson Cancer Research Center, Computational Biology Group, Fairview Avenue North, Seattle, WA 98109-1024, USA
| | - Wolfgang Huber
- EMBL, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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35
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Risk M, Coleman I, Dumpit R, Gentleman R, Kristal AR, Knudsen BS, Nelson PS, Lin DW. Differential gene expression in normal prostate epithelium of men with and without prostate cancer. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.5142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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36
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Abstract
We review the estimation of coverage and error rate in high-throughput protein-protein interaction datasets and argue that reports of the low quality of such data are to a substantial extent based on misinterpretations. Probabilistic statistical models and methods can be used to estimate properties of interest and to make the best use of the available data.
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37
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Abstract
UNLABELLED Automated analysis of flow cytometry (FCM) data is essential for it to become successful as a high throughput technology. We believe that the principles of Trellis graphics can be adapted to provide useful visualizations that can aid such automation. In this article, we describe the R/Bioconductor package flowViz that implements such visualizations. AVAILABILITY flowViz is available as an R package from the Bioconductor project: http://bioconductor.org
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Affiliation(s)
- D Sarkar
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.
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38
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Abstract
MOTIVATION Proteins work together to drive biological processes in cellular machines. Summarizing global and local properties of the set of protein interactions, the interactome, is necessary for describing cellular systems. We consider a relatively simple per-protein feature of the interactome: the number of interaction partners for a protein, which in graph terminology is the degree of the protein. RESULTS Using data subject to both stochastic and systematic sources of false positive and false negative observations, we develop an explicit probability model and resultant likelihood method to estimate node degree on portions of the interactome assayed by bait-prey technologies. This approach yields substantial improvement in degree estimation over the current practice that naively sums observed edges. Accurate modeling of observed data in relation to true but unknown parameters of interest gives a formal point of reference from which to draw conclusions about the system under study. AVAILABILITY All analyses discussed in this text can be performed using the ppiStats and ppiData packages available through the Bioconductor project (http://www.bioconductor.org).
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Affiliation(s)
- Denise Scholtens
- Department of Preventive Medicine, Northwestern University Medical School, 680 N. Lake Shore Drive Suite 1102, Chicago, IL 60611-4402, USA.
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Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, Huber W. Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Bioinformatics 2007; 24:1100-1. [PMID: 17989096 DOI: 10.1093/bioinformatics/btm518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The IntAct repository is one of the largest and most widely used databases for the curation and storage of molecular interaction data. These datasets need to be analyzed by computational methods. Software packages in the statistical environment R provide powerful tools for conducting such analyses. RESULTS We introduce Rintact, a Bioconductor package that allows users to transform PSI-MI XML2.5 interaction data files from IntAct into R graph objects. On these, they can use methods from R and Bioconductor for a variety of tasks: determining cohesive subgraphs, computing summary statistics, fitting mathematical models to the data or rendering graphical layouts. Rintact provides a programmatic interface to the IntAct repository and allows the use of the analytic methods provided by R and Bioconductor. AVAILABILITY Rintact is freely available at http://bioconductor.org
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Affiliation(s)
- Tony Chiang
- EBI-EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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40
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Abstract
Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network.
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Affiliation(s)
- Wolfgang Huber
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, UK
| | - Vincent J Carey
- Channing Laboratory, Brigham and Women's Hospital, 75 Francis Street, Boston MA 02115, USA
| | - Li Long
- Vital-IT Center, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Seth Falcon
- Fred Hutchinson Cancer Research Center, Computational Biology Group, 1100 Fairview Avenue North – M2-B876, P.O. Box 19024, Seattle WA 98109-1024, USA
| | - Robert Gentleman
- Fred Hutchinson Cancer Research Center, Computational Biology Group, 1100 Fairview Avenue North – M2-B876, P.O. Box 19024, Seattle WA 98109-1024, USA
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41
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Le Meur N, Rossini A, Gasparetto M, Smith C, Brinkman RR, Gentleman R. Data quality assessment of ungated flow cytometry data in high throughput experiments. Cytometry A 2007; 71:393-403. [PMID: 17366638 PMCID: PMC2768034 DOI: 10.1002/cyto.a.20396] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND The recent development of semiautomated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in the development of high throughput flow cytometry methods for data analysis and display. Especially, data quality control and quality assessment are crucial steps in processing and analyzing high throughput flow cytometry data. METHODS We propose a variety of graphical exploratory data analytic tools for exploring ungated flow cytometry data. We have implemented a number of specialized functions and methods in the Bioconductor package rflowcyt. We demonstrate the use of these approaches by investigating two independent sets of high throughput flow cytometry data. RESULTS We found that graphical representations can reveal substantial nonbiological differences in samples. Empirical Cumulative Distribution Function and summary scatterplots were especially useful in the rapid identification of problems not identified by manual review. CONCLUSIONS Graphical exploratory data analytic tools are quick and useful means of assessing data quality. We propose that the described visualizations should be used as quality assessment tools and where possible, be used for quality control.
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Affiliation(s)
- Nolwenn Le Meur
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
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42
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43
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Abstract
UNLABELLED This paper reviews the central concepts and implementation of data structures and methods for studying genetics of gene expression with the GGtools package of Bioconductor. Illustration with a HapMap+expression dataset is provided. AVAILABILITY Package GGtools is part of Bioconductor 1.9 (http://bioconductor.org). Open source with Artistic License.
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Affiliation(s)
- Vincent J Carey
- Channing Laboratory, Brigham and Women's Hospital, 75 Francis Street, Boston 02115, USA.
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44
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Abstract
MOTIVATION Gene Set Enrichment Analysis (GSEA) has been developed recently to capture changes in the expression of pre-defined sets of genes. We propose number of extensions to GSEA, including the use of different statistics to describe the association between genes and phenotypes of interest. We make use of dimension reduction procedures, such as principle component analysis, to identify gene sets with correlated expression. We also address issues that arise when gene sets overlap. RESULTS Our proposals extend the range of applicability of GSEA and allow for adjustments based on other covariates. We have provided a well-defined procedure to address interpretation issues that can raise when gene sets have substantial overlap. We have shown how standard dimension reduction methods, such as PCA, can be used to help further interpret GSEA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhen Jiang
- Computational Biology, 1100 Fairview Avenue. N. M2-B876, PO Box 19024, Seattle, WA 98109-1024, USA.
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45
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Abstract
MOTIVATION Functional analyses based on the association of Gene Ontology (GO) terms to genes in a selected gene list are useful bioinformatic tools and the GOstats package has been widely used to perform such computations. In this paper we report significant improvements and extensions such as support for conditional testing. RESULTS We discuss the capabilities of GOstats, a Bioconductor package written in R, that allows users to test GO terms for over or under-representation using either a classical hypergeometric test or a conditional hypergeometric that uses the relationships among GO terms to decorrelate the results. AVAILABILITY GOstats is available as an R package from the Bioconductor project: http://bioconductor.org
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Affiliation(s)
- S Falcon
- Fred Hutchison Cancer Research Center, Program Computational Biology,1100 Fairview Avenue North P. O. Box 19024, Seattle, WA 98109, USA.
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Shi Q, Harris LN, Lu X, Li X, Hwang J, Gentleman R, Iglehart JD, Miron A. Declining Plasma Fibrinogen Alpha Fragment Identifies HER2-Positive Breast Cancer Patients and Reverts to Normal Levels after Surgery. J Proteome Res 2006; 5:2947-55. [PMID: 17081046 DOI: 10.1021/pr060099u] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Breast cancer is the most common nonskin malignancy affecting women. Currently, no simple, blood-based diagnostic test exists to complement radiological screening and increase sensitivity of detection. To screen plasma specimens and identify biomarkers that detect HER2-positive breast cancer, automated robotic sample processing followed by surface-enhanced laser desorption ionization time-of-flight (SELDI-TOF) mass spectroscopy was used. Multiple statistical algorithms were used to select biomarkers that segregate cancer patients versus controls and produced average CV rates ranging from 20% to 29%. A set of seven biomarkers were validated on an independent test data set and achieved the best error rate of 19.1%. A permutation test indicated a p-value for CV error less than 0.002. Moreover, a ROC curve using these biomarkers achieved an area-under-the-curve value of 0.95 on an independent test data set. The marker responsible for most of the resolving power was identified as a fragment of Fibrinogen Alpha (FGA) encompassing residues 605-629. This marker was present at lower levels in cancer patients as compared to controls. The importance of this biomarker was validated in a longitudinal study comparing pre- and post-operative levels and was shown to revert to normal levels after surgery. This fragment may serve as a useful diagnostic and treatment-monitoring marker.
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Affiliation(s)
- Qian Shi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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47
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Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. Top-down standards will not serve systems biology. Nature 2006; 440:24. [PMID: 16511469 DOI: 10.1038/440024a] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gentleman R. Developing Statistical Software inFORTRAN 95. J Stat Softw 2006. [DOI: 10.18637/jss.v017.b02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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49
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Chiaretti S, Li X, Gentleman R, Vitale A, Wang KS, Mandelli F, Foà R, Ritz J. Gene Expression Profiles of B-lineage Adult Acute Lymphocytic Leukemia Reveal Genetic Patterns that Identify Lineage Derivation and Distinct Mechanisms of Transformation. Clin Cancer Res 2005; 11:7209-19. [PMID: 16243790 DOI: 10.1158/1078-0432.ccr-04-2165] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To characterize gene expression signatures in acute lymphocytic leukemia (ALL) cells associated with known genotypic abnormalities in adult patients. EXPERIMENTAL DESIGN Gene expression profiles from 128 adult patients with newly diagnosed ALL were characterized using high-density oligonucleotide microarrays. All patients were enrolled in the Italian GIMEMA multicenter clinical trial 0496 and samples had >90% leukemic cells. Uniform phenotypic, cytogenetic, and molecular data were also available for all cases. RESULTS T-lineage ALL was characterized by a homogeneous gene expression pattern, whereas several subgroups of B-lineage ALL were evident. Within B-lineage ALL, distinct signatures were associated with ALL1/AF4 and E2A/PBX1 gene rearrangements. Expression profiles associated with ALL1/AF4 and E2A/PBX1 are similar in adults and children. BCR/ABL+ gene expression pattern was more heterogeneous and was most similar to ALL without known molecular rearrangements. We also identified a set of 83 genes that were highly expressed in leukemia blasts from patients without known molecular abnormalities who subsequently relapsed following therapy. Supervised analysis of kinase genes revealed a high-level FLT3 expression in a subset of cases without molecular rearrangements. Two other kinases (PRKCB1 and DDR1) were highly expressed in cases without molecular rearrangements, as well as in BCR/ABL-positive ALL. CONCLUSIONS Genomic signatures are associated with phenotypically and molecularly well defined subgroups of adult ALL. Genomic profiling also identifies genes associated with poor outcome in cases without molecular aberrations and specific genes that may be new therapeutic targets in adult ALL.
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Affiliation(s)
- Sabina Chiaretti
- Department of Medical Oncology and Biostatistical Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
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50
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Abstract
DNA microarrays in conjunction with statistical models may help gain a deeper understanding of the molecular basis for specific diseases. An intense area of research is concerned with the identification of genes related to particular phenotypes. The technology, however, is subject to various sources of error that may lead to expression readings that are substantially different from the true transcript levels. Few methods for microarray data analysis have accounted for measurement error in a substantial way and that is the purpose of this investigation. We describe a Bayesian error-in-variable model for the analysis of microarray data from a clinical study of patients with acute lymphoblastic leukemia. We focus in particular on the problem of identifying genes whose expression patterns are associated with duration of remission. This is a question of great practical interest since relapse is a major concern in the treatment of this disease. We explore the effects of ignoring the uncertainty in the expression estimates on the selection and ranking of genes.
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Affiliation(s)
- Mahlet G Tadesse
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6021, USA.
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