1
|
Ochoa D, Hercules A, Carmona M, Suveges D, Gonzalez-Uriarte A, Malangone C, Miranda A, Fumis L, Carvalho-Silva D, Spitzer M, Baker J, Ferrer J, Raies A, Razuvayevskaya O, Faulconbridge A, Petsalaki E, Mutowo P, Machlitt-Northen S, Peat G, McAuley E, Ong CK, Mountjoy E, Ghoussaini M, Pierleoni A, Papa E, Pignatelli M, Koscielny G, Karim M, Schwartzentruber J, Hulcoop DG, Dunham I, McDonagh EM. Open Targets Platform: supporting systematic drug-target identification and prioritisation. Nucleic Acids Res 2021; 49:D1302-D1310. [PMID: 33196847 PMCID: PMC7779013 DOI: 10.1093/nar/gkaa1027] [Citation(s) in RCA: 192] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence. It is publicly available and the underlying code is open source. Since our last update two years ago, we have had 10 releases to maintain and continuously improve evidence for target-disease relationships from 20 different data sources. In addition, we have integrated new evidence from key datasets, including prioritised targets identified from genome-wide CRISPR knockout screens in 300 cancer models (Project Score), and GWAS/UK BioBank statistical genetic analysis evidence from the Open Targets Genetics Portal. We have evolved our evidence scoring framework to improve target identification. To aid the prioritisation of targets and inform on the potential impact of modulating a given target, we have added evaluation of post-marketing adverse drug reactions and new curated information on target tractability and safety. We have also developed the user interface and backend technologies to improve performance and usability. In this article, we describe the latest enhancements to the Platform, to address the fundamental challenge that developing effective and safe drugs is difficult and expensive.
Collapse
Affiliation(s)
- David Ochoa
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Andrew Hercules
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Miguel Carmona
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Daniel Suveges
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Asier Gonzalez-Uriarte
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Cinzia Malangone
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alfredo Miranda
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Luca Fumis
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Michaela Spitzer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jarrod Baker
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Javier Ferrer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Arwa Raies
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Olesya Razuvayevskaya
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Adam Faulconbridge
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eirini Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Prudence Mutowo
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Sandra Machlitt-Northen
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Gareth Peat
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Elaine McAuley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Chuang Kee Ong
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Edward Mountjoy
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Maya Ghoussaini
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andrea Pierleoni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eliseo Papa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Systems Biology, Biogen, Cambridge, MA 02142, USA
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gautier Koscielny
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Mohd Karim
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jeremy Schwartzentruber
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David G Hulcoop
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| |
Collapse
|
2
|
Dwane L, Behan FM, Gonçalves E, Lightfoot H, Yang W, van der Meer D, Shepherd R, Pignatelli M, Iorio F, Garnett MJ. Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets. Nucleic Acids Res 2021. [PMID: 33068406 DOI: 10.6084/m9.figshare.16924132.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
CRISPR genetic screens in cancer cell models are a powerful tool to elucidate oncogenic mechanisms and to identify promising therapeutic targets. The Project Score database (https://score.depmap.sanger.ac.uk/) uses genome-wide CRISPR-Cas9 dropout screening data in hundreds of highly annotated cancer cell models to identify genes required for cell fitness and prioritize novel oncology targets. The Project Score database currently allows users to investigate the fitness effect of 18 009 genes tested across 323 cancer cell models. Through interactive interfaces, users can investigate data by selecting a specific gene, cancer cell model or tissue type, as well as browsing all gene fitness scores. Additionally, users can identify and rank candidate drug targets based on an established oncology target prioritization pipeline, incorporating genetic biomarkers and clinical datasets for each target, and including suitability for drug development based on pharmaceutical tractability. Data are freely available and downloadable. To enhance analyses, links to other key resources including Open Targets, COSMIC, the Cell Model Passports, UniProt and the Genomics of Drug Sensitivity in Cancer are provided. The Project Score database is a valuable new tool for investigating genetic dependencies in cancer cells and the identification of candidate oncology targets.
Collapse
Affiliation(s)
- Lisa Dwane
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fiona M Behan
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | | | - Wanjuan Yang
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | | | | | - Francesco Iorio
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Human Technopole, 20157 Milano, Italy
| | - Mathew J Garnett
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| |
Collapse
|
3
|
Dwane L, Behan FM, Gonçalves E, Lightfoot H, Yang W, van der Meer D, Shepherd R, Pignatelli M, Iorio F, Garnett MJ. Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets. Nucleic Acids Res 2021; 49:D1365-D1372. [PMID: 33068406 PMCID: PMC7778984 DOI: 10.1093/nar/gkaa882] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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] [Received: 08/14/2020] [Revised: 09/22/2020] [Accepted: 10/14/2020] [Indexed: 01/10/2023] Open
Abstract
CRISPR genetic screens in cancer cell models are a powerful tool to elucidate oncogenic mechanisms and to identify promising therapeutic targets. The Project Score database (https://score.depmap.sanger.ac.uk/) uses genome-wide CRISPR-Cas9 dropout screening data in hundreds of highly annotated cancer cell models to identify genes required for cell fitness and prioritize novel oncology targets. The Project Score database currently allows users to investigate the fitness effect of 18 009 genes tested across 323 cancer cell models. Through interactive interfaces, users can investigate data by selecting a specific gene, cancer cell model or tissue type, as well as browsing all gene fitness scores. Additionally, users can identify and rank candidate drug targets based on an established oncology target prioritization pipeline, incorporating genetic biomarkers and clinical datasets for each target, and including suitability for drug development based on pharmaceutical tractability. Data are freely available and downloadable. To enhance analyses, links to other key resources including Open Targets, COSMIC, the Cell Model Passports, UniProt and the Genomics of Drug Sensitivity in Cancer are provided. The Project Score database is a valuable new tool for investigating genetic dependencies in cancer cells and the identification of candidate oncology targets.
Collapse
Affiliation(s)
- Lisa Dwane
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fiona M Behan
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | | | - Wanjuan Yang
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | | | | | - Francesco Iorio
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Human Technopole, 20157 Milano, Italy
| | - Mathew J Garnett
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| |
Collapse
|
4
|
Train CM, Pignatelli M, Altenhoff A, Dessimoz C. iHam and pyHam: visualizing and processing hierarchical orthologous groups. Bioinformatics 2020; 35:2504-2506. [PMID: 30508066 PMCID: PMC6612847 DOI: 10.1093/bioinformatics/bty994] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 05/09/2018] [Revised: 11/24/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Summary The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species. Availability and implementation iHam’s code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam’s code is available at https://github.com/DessimozLab/pyHam and or via the pip package ‘pyham’.
Collapse
Affiliation(s)
- Clément-Marie Train
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,ETH Zurich, Department of Computer Science, Zurich, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Miguel Pignatelli
- Open Targets.,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Adrian Altenhoff
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,ETH Zurich, Department of Computer Science, Zurich, Switzerland
| | - Christophe Dessimoz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Department of Genetics, Evolution and Environment, University College London, London, UK.,Department of Computer Science, University College London, London, UK
| |
Collapse
|
5
|
Carvalho-Silva D, Pierleoni A, Pignatelli M, Ong C, Fumis L, Karamanis N, Carmona M, Faulconbridge A, Hercules A, McAuley E, Miranda A, Peat G, Spitzer M, Barrett J, Hulcoop DG, Papa E, Koscielny G, Dunham I. Open Targets Platform: new developments and updates two years on. Nucleic Acids Res 2020; 47:D1056-D1065. [PMID: 30462303 PMCID: PMC6324073 DOI: 10.1093/nar/gky1133] [Citation(s) in RCA: 269] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022] Open
Abstract
The Open Targets Platform integrates evidence from genetics, genomics, transcriptomics, drugs, animal models and scientific literature to score and rank target-disease associations for drug target identification. The associations are displayed in an intuitive user interface (https://www.targetvalidation.org), and are available through a REST-API (https://api.opentargets.io/v3/platform/docs/swagger-ui) and a bulk download (https://www.targetvalidation.org/downloads/data). In addition to target-disease associations, we also aggregate and display data at the target and disease levels to aid target prioritisation. Since our first publication two years ago, we have made eight releases, added new data sources for target-disease associations, started including causal genetic variants from non genome-wide targeted arrays, added new target and disease annotations, launched new visualisations and improved existing ones and released a new web tool for batch search of up to 200 targets. We have a new URL for the Open Targets Platform REST-API, new REST endpoints and also removed the need for authorisation for API fair use. Here, we present the latest developments of the Open Targets Platform, expanding the evidence and target-disease associations with new and improved data sources, refining data quality, enhancing website usability, and increasing our user base with our training workshops, user support, social media and bioinformatics forum engagement.
Collapse
Affiliation(s)
- Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Andrea Pierleoni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - ChuangKee Ong
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Luca Fumis
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Nikiforos Karamanis
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Miguel Carmona
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Adam Faulconbridge
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Andrew Hercules
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Elaine McAuley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alfredo Miranda
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gareth Peat
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Michaela Spitzer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jeffrey Barrett
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David G Hulcoop
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,GSK, Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Eliseo Papa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - Gautier Koscielny
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,GSK, Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| |
Collapse
|
6
|
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J. Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer. Cancer Res 2017; 78:769-780. [PMID: 29229604 DOI: 10.1158/0008-5472.can-17-1679] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/16/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022]
Abstract
Transcriptional dysregulation induced by aberrant transcription factors (TF) is a key feature of cancer, but its global influence on drug sensitivity has not been examined. Here, we infer the transcriptional activity of 127 TFs through analysis of RNA-seq gene expression data newly generated for 448 cancer cell lines, combined with publicly available datasets to survey a total of 1,056 cancer cell lines and 9,250 primary tumors. Predicted TF activities are supported by their agreement with independent shRNA essentiality profiles and homozygous gene deletions, and recapitulate mutant-specific mechanisms of transcriptional dysregulation in cancer. By analyzing cell line responses to 265 compounds, we uncovered numerous TFs whose activity interacts with anticancer drugs. Importantly, combining existing pharmacogenomic markers with TF activities often improves the stratification of cell lines in response to drug treatment. Our results, which can be queried freely at dorothea.opentargets.io, offer a broad foundation for discovering opportunities to refine personalized cancer therapies.Significance: Systematic analysis of transcriptional dysregulation in cancer cell lines and patient tumor specimens offers a publicly searchable foundation to discover new opportunities to refine personalized cancer therapies. Cancer Res; 78(3); 769-80. ©2017 AACR.
Collapse
Affiliation(s)
- Luz Garcia-Alonso
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom.,OpenTargets, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Francesco Iorio
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom.,OpenTargets, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Angela Matchan
- OpenTargets, Wellcome Genome Campus, Cambridge, United Kingdom.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Nuno Fonseca
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Patricia Jaaks
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Gareth Peat
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom.,OpenTargets, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Miguel Pignatelli
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom.,OpenTargets, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Fiammetta Falcone
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - Cyril H Benes
- Massachusetts General Hospital, Boston, Massachusetts
| | - Ian Dunham
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom.,OpenTargets, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Graham Bignell
- OpenTargets, Wellcome Genome Campus, Cambridge, United Kingdom.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Simon S McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - Mathew J Garnett
- OpenTargets, Wellcome Genome Campus, Cambridge, United Kingdom.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom. .,OpenTargets, Wellcome Genome Campus, Cambridge, United Kingdom.,Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany
| |
Collapse
|
7
|
Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I. Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res 2016; 45:D985-D994. [PMID: 27899665 PMCID: PMC5210543 DOI: 10.1093/nar/gkw1055] [Citation(s) in RCA: 267] [Impact Index Per Article: 33.4] [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: 08/19/2016] [Revised: 10/19/2016] [Accepted: 11/03/2016] [Indexed: 01/16/2023] Open
Abstract
We have designed and developed a data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources. The platform provides either a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease. Users can easily transition between these target- and disease-centric workflows. The Open Targets Validation Platform is accessible at https://www.targetvalidation.org.
Collapse
Affiliation(s)
- Gautier Koscielny
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK .,GSK, Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Peter An
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - Denise Carvalho-Silva
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jennifer A Cham
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Luca Fumis
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Rippa Gasparyan
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - Samiul Hasan
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,GSK, Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Nikiforos Karamanis
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Michael Maguire
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Eliseo Papa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - Andrea Pierleoni
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Miguel Pignatelli
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Theo Platt
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - Francis Rowland
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Priyanka Wankar
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - A Patrícia Bento
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tony Burdett
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Antonio Fabregat
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Simon Forbes
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anna Gaulton
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Cristina Yenyxe Gonzalez
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Henning Hermjakob
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,National Center for Protein Research, No. 38, Life Science Park Road, Changping District, 102206 Beijing, China
| | - Anne Hersey
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Steven Jupe
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Şenay Kafkas
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Keays
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Catherine Leroy
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Francisco-Javier Lopez
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Paula Magarinos
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - James Malone
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Johanna McEntyre
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alfonso Munoz-Pomer Fuentes
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Claire O'Donovan
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Irene Papatheodorou
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Helen Parkinson
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Barbara Palka
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Justin Paschall
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Robert Petryszak
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Naruemon Pratanwanich
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sirarat Sarntivijal
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Gary Saunders
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Konstantinos Sidiropoulos
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Thomas Smith
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Zbyslaw Sondka
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Oliver Stegle
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Y Amy Tang
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Edward Turner
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Brendan Vaughan
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Olga Vrousgou
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Xavier Watkins
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria-Jesus Martin
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Philippe Sanseau
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,GSK, Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Jessica Vamathevan
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ewan Birney
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jeffrey Barrett
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ian Dunham
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK .,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| |
Collapse
|
8
|
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SMJ, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Ensembl comparative genomics resources. Database (Oxford) 2016; 2016:baw053. [PMID: 27141089 PMCID: PMC4852398 DOI: 10.1093/database/baw053] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
9
|
Abstract
UNLABELLED There is an increasing need for rich and dynamic biological data visualizations in bioinformatic web applications. New standards in web technologies, like SVG or Canvas, are now supported by most modern web browsers allowing the blossoming of powerful visualizations in biological data analysis. The exploration of different ways to visualize genomic data is still challenging due to the lack of flexible tools to develop them. Here, I present a set of libraries aimed at creating powerful tree- and track-based visualizations for the web. Its modularity and rich API facilitate the development of many different visualizations ranging from simple species trees to complex visualizations comprising per-node data annotations or even simple genome browsers. AVAILABILITY AND IMPLEMENTATION The TnT libraries have been written in Javascript, licensed under the APACHE 2.0 license and hosted at https://github.com/tntvis CONTACT mp@ebi.ac.uk.
Collapse
Affiliation(s)
- Miguel Pignatelli
- Centre for Therapeutic Target Validation and European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| |
Collapse
|
10
|
Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P, Herrero J. ncRNA orthologies in the vertebrate lineage. Database (Oxford) 2016; 2016:bav127. [PMID: 26980512 PMCID: PMC4792531 DOI: 10.1093/database/bav127] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 01/07/2023]
Abstract
Annotation of orthologous and paralogous genes is necessary for many aspects of evolutionary analysis. Methods to infer these homology relationships have traditionally focused on protein-coding genes and evolutionary models used by these methods normally assume the positions in the protein evolve independently. However, as our appreciation for the roles of non-coding RNA genes has increased, consistently annotated sets of orthologous and paralogous ncRNA genes are increasingly needed. At the same time, methods such as PHASE or RAxML have implemented substitution models that consider pairs of sites to enable proper modelling of the loops and other features of RNA secondary structure. Here, we present a comprehensive analysis pipeline for the automatic detection of orthologues and paralogues for ncRNA genes. We focus on gene families represented in Rfam and for which a specific covariance model is provided. For each family ncRNA genes found in all Ensembl species are aligned using Infernal, and several trees are built using different substitution models. In parallel, a genomic alignment that includes the ncRNA genes and their flanking sequence regions is built with PRANK. This alignment is used to create two additional phylogenetic trees using the neighbour-joining (NJ) and maximum-likelihood (ML) methods. The trees arising from both the ncRNA and genomic alignments are merged using TreeBeST, which reconciles them with the species tree in order to identify speciation and duplication events. The final tree is used to infer the orthologues and paralogues following Fitch's definition. We also determine gene gain and loss events for each family using CAFE. All data are accessible through the Ensembl Comparative Genomics ('Compara') API, on our FTP site and are fully integrated in the Ensembl genome browser, where they can be accessed in a user-friendly manner. Database URL: http://www.ensembl.org.
Collapse
Affiliation(s)
- Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute
| | - Albert J Vilella
- European Molecular Biology Laboratory, European Bioinformatics Institute
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute
| | - Simon White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Javier Herrero
- European Molecular Biology Laboratory, European Bioinformatics Institute UCL Cancer Institute, University College London, London WC1E 6BT, UK
| |
Collapse
|
11
|
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SMJ, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Ensembl comparative genomics resources. Database (Oxford) 2016; 2016:bav096. [PMID: 26896847 PMCID: PMC4761110 DOI: 10.1093/database/bav096] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [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] [Received: 05/02/2015] [Revised: 08/10/2015] [Accepted: 09/04/2015] [Indexed: 01/08/2023]
Abstract
Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org.
Collapse
Affiliation(s)
- Javier Herrero
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
| | - Stephen Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
| | - Albert J. Vilella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
| | | | - Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA
| | - Simon Brent
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA
| | - William Spooner
- Eagle Genomics Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK, and
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Eugene Kulesha
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA
| |
Collapse
|
12
|
Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P. Ensembl 2016. Nucleic Acids Res 2016; 44:D710-6. [PMID: 26687719 PMCID: PMC4702834 DOI: 10.1093/nar/gkv1157] [Citation(s) in RCA: 1066] [Impact Index Per Article: 133.3] [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] [Received: 09/19/2015] [Revised: 10/19/2015] [Accepted: 10/19/2015] [Indexed: 01/17/2023] Open
Abstract
The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.
Collapse
Affiliation(s)
- Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Clapham
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nathan Johnson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Nuhn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Rahtz
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Harpreet Singh Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven P Wilder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Giulietta Spudich
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| |
Collapse
|
13
|
Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JMA, Bertelsen MF, Murchison EP, Flicek P, Odom DT. Enhancer evolution across 20 mammalian species. Cell 2015; 160:554-66. [PMID: 25635462 PMCID: PMC4313353 DOI: 10.1016/j.cell.2015.01.006] [Citation(s) in RCA: 445] [Impact Index Per Article: 49.4] [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] [Received: 08/29/2014] [Revised: 10/31/2014] [Accepted: 12/15/2014] [Indexed: 12/21/2022]
Abstract
The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution.
Collapse
Affiliation(s)
- Diego Villar
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Camille Berthelot
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sarah Aldridge
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Tim F Rayner
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Margus Lukk
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Thomas J Park
- Department of Biological Sciences, University of Illinois at Chicago (UIC), 845 West Taylor Street, Chicago, IL 60607, USA
| | - Robert Deaville
- UK Cetacean Strandings Investigation Programme (CSIP) and Institute of Zoology, Zoological Society of London, Outer Circle, Regent's Park, London NW1 4RY, UK
| | - Jonathan T Erichsen
- School of Optometry and Vision Sciences, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
| | - Anna J Jasinska
- UCLA Center for Neurobehavioral Genetics, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - James M A Turner
- Division of Stem Cell Biology and Developmental Genetics, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Mads F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Elizabeth P Murchison
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| |
Collapse
|
14
|
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B. A comparative encyclopedia of DNA elements in the mouse genome. Nature 2015; 515:355-64. [PMID: 25409824 PMCID: PMC4266106 DOI: 10.1038/nature13992] [Citation(s) in RCA: 1135] [Impact Index Per Article: 126.1] [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: 02/03/2014] [Accepted: 10/24/2014] [Indexed: 12/11/2022]
Abstract
The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.
Collapse
Affiliation(s)
- Feng Yue
- 1] Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA
| | - Yong Cheng
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Alessandra Breschi
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Weisheng Wu
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Tyrone Ryba
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Zhihai Ma
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Carrie Davis
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Benjamin D Pope
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Yin Shen
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Dmitri D Pervouchine
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Sarah Djebali
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Rajinder Kaul
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Eric Rynes
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Anthony Kirilusha
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Georgi K Marinov
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Brian A Williams
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Diane Trout
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Henry Amrhein
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Katherine Fisher-Aylor
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Igor Antoshechkin
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Gilberto DeSalvo
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Lei-Hoon See
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Meagan Fastuca
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Jorg Drenkow
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Chris Zaleski
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Alex Dobin
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Pablo Prieto
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Julien Lagarde
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Giovanni Bussotti
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Andrea Tanzer
- 1] Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain. [2] Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17/3/303, A-1090 Vienna, Austria
| | - Olgert Denas
- Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA
| | - Kanwei Li
- Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA
| | - M A Bender
- 1] Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA. [2] Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Miaohua Zhang
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Rachel Byron
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Mark T Groudine
- 1] Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. [2] Department of Radiation Oncology, University of Washington, Seattle, Washington 98195, USA
| | - David McCleary
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Long Pham
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Samantha Kuan
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Lee Edsall
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Yi-Chieh Wu
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Matthew D Rasmussen
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Mukul S Bansal
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Manolis Kellis
- 1] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Cheryl A Keller
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Christapher S Morrissey
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Tejaswini Mishra
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Deepti Jain
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nergiz Dogan
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Robert S Harris
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip Cayting
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Trupti Kawli
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Alan P Boyle
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Ghia Euskirchen
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Shin Lin
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Yiing Lin
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Camden Jansen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA
| | - Venkat S Malladi
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Melissa S Cline
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
| | - Drew T Erickson
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Vanessa M Kirkup
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
| | - Katrina Learned
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Kate R Rosenbloom
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
| | - Beatriz Lacerda de Sousa
- Departments of Obstetrics/Gynecology and Pathology, and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jin Lian
- Yale University, Department of Genetics, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA
| | - Tamer Kahveci
- Computer &Information Sciences &Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Dongwon Lee
- McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA
| | - W James Kent
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
| | - Miguel Ramalho Santos
- Departments of Obstetrics/Gynecology and Pathology, and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA
| | - Javier Herrero
- 1] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [2] Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Cedric Notredame
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Audra Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Fidencio Neri
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Theresa Canfield
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Anthony Shafer
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Tanya Kutyavin
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Alex P Reynolds
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - R Scott Hansen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Marella De Bruijn
- MRC Molecular Haemotology Unit, University of Oxford, Oxford OX3 9DS, UK
| | - Licia Selleri
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Alexander Rudensky
- HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA
| | - Steven Josefowicz
- HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA
| | - Robert Samstein
- HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Stuart H Orkin
- Dana Farber Cancer Institute, Harvard Medical School, Cambridge, Massachusetts 02138, USA
| | - Dana Levasseur
- University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, Iowa 52242, USA
| | - Thalia Papayannopoulou
- Division of Hematology, Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Kai-Hsin Chang
- University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, Iowa 52242, USA
| | - Arthur Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Srikanta Gosh
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Christine Disteche
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Piper Treuting
- Department of Comparative Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Yanli Wang
- Bioinformatics and Genomics program, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Mitchell J Weiss
- Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Gerd A Blobel
- 1] Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA. [2] Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Xiaoyi Cao
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Peter J Good
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Rebecca F Lowdon
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Leslie B Adams
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Xiao-Qiao Zhou
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Michael J Pazin
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Elise A Feingold
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Barbara Wold
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - James Taylor
- Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA
| | - Sherman M Weissman
- Yale University, Department of Genetics, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Roderic Guigo
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Thomas R Gingeras
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - David M Gilbert
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael A Beer
- McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | | |
Collapse
|
15
|
Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SMJ, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P. Ensembl 2015. Nucleic Acids Res 2014; 43:D662-9. [PMID: 25352552 PMCID: PMC4383879 DOI: 10.1093/nar/gku1010] [Citation(s) in RCA: 961] [Impact Index Per Article: 96.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license.
Collapse
Affiliation(s)
- Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Brent
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Clapham
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Guy Coates
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nathan Johnson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andreas K Kähäri
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bert Overduin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Harpreet Singh Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven P Wilder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rhoda Kinsella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Giulietta Spudich
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andy Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| |
Collapse
|
16
|
McDonald M, Kanter S, Pignatelli M, Khamzina N, Mahoney J, Woodward J. Developing a new medical school at a new university in Kazakhstan. Ann Glob Health 2014. [DOI: 10.1016/j.aogh.2014.08.100] [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: 10/24/2022] Open
|
17
|
Yates A, Beal K, Keenan S, McLaren W, Pignatelli M, Ritchie GRS, Ruffier M, Taylor K, Vullo A, Flicek P. The Ensembl REST API: Ensembl Data for Any Language. ACTA ACUST UNITED AC 2014; 31:143-5. [PMID: 25236461 PMCID: PMC4271150 DOI: 10.1093/bioinformatics/btu613] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language. AVAILABILITY AND IMPLEMENTATION The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest.
Collapse
Affiliation(s)
- Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Graham R S Ritchie
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| |
Collapse
|
18
|
Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, Pignatelli M, Herrero J, Beal K, Nozawa M, Li Q, Wang J, Zhang H, Yu L, Shigenobu S, Wang J, Liu J, Flicek P, Searle S, Wang J, Kuratani S, Yin Y, Aken B, Zhang G, Irie N. Erratum: Corrigendum: The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet 2014. [DOI: 10.1038/ng0614-657a] [Citation(s) in RCA: 4] [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: 11/09/2022]
|
19
|
Martella G, Maltese M, Nisticò R, Schirinzi T, Madeo G, Sciamanna G, Ponterio G, Tassone A, Mandolesi G, Vanni V, Pignatelli M, Bonsi P, Pisani A. Regional specificity of synaptic plasticity deficits in a knock-in mouse model of DYT1 dystonia. Neurobiol Dis 2014; 65:124-32. [PMID: 24503369 DOI: 10.1016/j.nbd.2014.01.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 01/24/2014] [Indexed: 01/07/2023] Open
Abstract
DYT1 dystonia is a movement disorder caused by a deletion in the C-terminal of the protein torsinA. It is unclear how torsinA mutation might disrupt cellular processes encoding motor activity, and whether this impairment occurs in specific brain regions. Here, we report a selective impairment of corticostriatal synaptic plasticity in knock-in mice heterozygous for Δ-torsinA (Tor1a(+/Δgag) mice) as compared to controls (Tor1a(+/+) mice). In striatal spiny neurons from Tor1a(+/Δgag) mice, high-frequency stimulation failed to induce long-term depression (LTD), whereas long-term potentiation (LTP) exhibited increased amplitude. Of interest, blockade of D2 dopamine receptors (D2Rs) increased LTP in Tor1a(+/+) mice to a level comparable to that measured in Tor1a(+/Δgag) mice and normalized the levels of potentiation across mouse groups. A low-frequency stimulation (LFS) protocol was unable to depotentiate corticostriatal synapses in Tor1a(+/Δgag) mice. Muscarinic M1 acetylcholine receptor (mAChR) blockade rescued plasticity deficits. Additionally, we found an abnormal responsiveness of cholinergic interneurons to D2R activation, consisting in an excitatory response rather than the expected inhibition, further confirming an imbalance between dopaminergic and cholinergic signaling in the striatum. Conversely, synaptic activity and plasticity in the CA1 hippocampal region were unaltered in Tor1a(+/Δgag) mice. Importantly, the M1 mAChR-dependent enhancement of hippocampal LTP was unaffected in both genotypes. Similarly, both basic properties of dopaminergic nigral neurons and their responses to D2R activation were normal. These results provide evidence for a regional specificity of the electrophysiological abnormalities observed and demonstrate the reproducibility of such alterations in distinct models of DYT1 dystonia.
Collapse
Affiliation(s)
- G Martella
- Department of System Medicine, University of Rome "Tor Vergata", Italy; Laboratory of Neurophysiology and Synaptic Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - M Maltese
- Department of System Medicine, University of Rome "Tor Vergata", Italy
| | - R Nisticò
- Laboratory of Neurophysiology and Synaptic Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy; Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, Italy
| | - T Schirinzi
- Department of System Medicine, University of Rome "Tor Vergata", Italy
| | - G Madeo
- Department of System Medicine, University of Rome "Tor Vergata", Italy
| | - G Sciamanna
- Department of System Medicine, University of Rome "Tor Vergata", Italy; Laboratory of Neurophysiology and Synaptic Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - G Ponterio
- Department of System Medicine, University of Rome "Tor Vergata", Italy; Laboratory of Neurophysiology and Synaptic Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - A Tassone
- Laboratory of Neurophysiology and Synaptic Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - G Mandolesi
- Department of System Medicine, University of Rome "Tor Vergata", Italy; Laboratory of Neurophysiology and Synaptic Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - V Vanni
- Laboratory of Neurophysiology and Synaptic Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - M Pignatelli
- Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, Italy
| | - P Bonsi
- Laboratory of Neurophysiology and Synaptic Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - A Pisani
- Department of System Medicine, University of Rome "Tor Vergata", Italy; Laboratory of Neurophysiology and Synaptic Plasticity, IRCCS Fondazione Santa Lucia, Rome, Italy.
| |
Collapse
|
20
|
Vázquez-Castellanos JF, García-López R, Pérez-Brocal V, Pignatelli M, Moya A. Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut. BMC Genomics 2014; 15:37. [PMID: 24438450 PMCID: PMC3901335 DOI: 10.1186/1471-2164-15-37] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 01/16/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sensitive methods for homology detection. This study compares the performance of different available assemblers and taxonomic annotation software using simulated viral-metagenomic data. RESULTS We simulated two 454 viral metagenomes using genomes from NCBI's RefSeq database based on the list of actual viruses found in previously published metagenomes. Three different assembly strategies, spanning six assemblers, were tested for performance: overlap-layout-consensus algorithms Newbler, Celera and Minimo; de Bruijn graphs algorithms Velvet and MetaVelvet; and read probabilistic model Genovo. The performance of the assemblies was measured by the length of resulting contigs (using N50), the percentage of reads assembled and the overall accuracy when comparing against corresponding reference genomes. Additionally, the number of chimeras per contig and the lowest common ancestor were estimated in order to assess the effect of assembling on taxonomic and functional annotation. The functional classification of the reads was evaluated by counting the reads that correctly matched the functional data previously reported for the original genomes and calculating the number of over-represented functional categories in chimeric contigs. The sensitivity and specificity of tBLASTx, PhymmBL and the k-mer frequencies were measured by accurate predictions when comparing simulated reads against the NCBI Virus genomes RefSeq database. CONCLUSIONS Assembling improves functional annotation by increasing accurate assignations and decreasing ambiguous hits between viruses and bacteria. However, the success is limited by the chimeric contigs occurring at all taxonomic levels. The assembler and its parameters should be selected based on the focus of each study. Minimo's non-chimeric contigs and Genovo's long contigs excelled in taxonomy assignation and functional annotation, respectively.tBLASTx stood out as the best approach for taxonomic annotation for virus identification. PhymmBL proved useful in datasets in which no related sequences are present as it uses genomic features that may help identify distant taxa. The k-frequencies underperformed in all viral datasets.
Collapse
Affiliation(s)
- Jorge F Vázquez-Castellanos
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valencia (FISABIO)-Salud Pública, Avenida de Cataluña 21, 46020 Valencia, Spain
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, Apartado Postal 22085, 46071 Valencia, Spain
| | - Rodrigo García-López
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valencia (FISABIO)-Salud Pública, Avenida de Cataluña 21, 46020 Valencia, Spain
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, Apartado Postal 22085, 46071 Valencia, Spain
| | - Vicente Pérez-Brocal
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valencia (FISABIO)-Salud Pública, Avenida de Cataluña 21, 46020 Valencia, Spain
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, Apartado Postal 22085, 46071 Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valencia (FISABIO)-Salud Pública, Avenida de Cataluña 21, 46020 Valencia, Spain
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, (ICBiBE) Universitat de València, Apartado Postal 22085, 46071 Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| |
Collapse
|
21
|
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJ, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Zerbino DR, Searle SM. Ensembl 2014. Nucleic Acids Res 2013; 42:D749-55. [PMID: 24316576 PMCID: PMC3964975 DOI: 10.1093/nar/gkt1196] [Citation(s) in RCA: 1056] [Impact Index Per Article: 96.0] [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: 02/06/2023] Open
Abstract
Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.
Collapse
Affiliation(s)
- Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- *To whom correspondence should be addressed. Tel: +44 1223 492 581; Fax: +44 1223 494 494;
| | - M. Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Brent
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Peter Clapham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Guy Coates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sarah Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Nathan Johnson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Andreas K. Kähäri
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Eugene Kulesha
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - William M. McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel N. Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Bert Overduin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Bethan Pritchard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Emily Pritchard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Harpreet S. Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen J. Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Steven P. Wilder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Mark Wilson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Bronwen L. Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jennifer Harrow
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Javier Herrero
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tim J.P. Hubbard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rhoda Kinsella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Giulietta Spudich
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Andy Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel R. Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen M.J. Searle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| |
Collapse
|
22
|
Abstract
TreeFam (http://www.treefam.org) is a database of phylogenetic trees inferred from animal genomes. For every TreeFam family we provide homology predictions together with the evolutionary history of the genes. Here we describe an update of the TreeFam database. The TreeFam project was resurrected in 2012 and has seen two releases since. The latest release (TreeFam 9) was made available in March 2013. It has orthology predictions and gene trees for 109 species in 15 736 families covering ∼2.2 million sequences. With release 9 we made modifications to our production pipeline and redesigned our website with improved gene tree visualizations and Wikipedia integration. Furthermore, we now provide an HMM-based sequence search that places a user-provided protein sequence into a TreeFam gene tree and provides quick orthology prediction. The tool uses Mafft and RAxML for the fast insertion into a reference alignment and tree, respectively. Besides the aforementioned technical improvements, we present a new approach to visualize gene trees and alternative displays that focuses on showing homology information from a species tree point of view. From release 9 onwards, TreeFam is now hosted at the EBI.
Collapse
Affiliation(s)
- Fabian Schreiber
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | | | | | | |
Collapse
|
23
|
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SMJ, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet 2013; 45:415-21, 421e1-2. [PMID: 23435085 PMCID: PMC3709584 DOI: 10.1038/ng.2568] [Citation(s) in RCA: 429] [Impact Index Per Article: 39.0] [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] [Received: 07/20/2012] [Accepted: 01/31/2013] [Indexed: 12/19/2022]
Abstract
Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ∼500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms.
Collapse
Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GRS, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJP, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Zadissa A, Searle SMJ. Ensembl 2013. Nucleic Acids Res 2012. [PMID: 23203987 PMCID: PMC3531136 DOI: 10.1093/nar/gks1236] [Citation(s) in RCA: 787] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.
Collapse
Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Jankowski J, Newham P, Kandemir O, Hirano S, Takeichi M, Pignatelli M. Differential expression of e-cadherin in normal, metaplastic and dysplastic esophageal mucosa - a putative biomarker. Int J Oncol 2012; 4:441-8. [PMID: 21566944 DOI: 10.3892/ijo.4.2.441] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [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] Open
Abstract
Barrett's mucosa is a potentially premalignant columnar lined metaplastic epithelium in the oesophagus about which little is known regarding maintenance of cell adhesion. In this regard E-Cadherin (E-cad) is a 120 kDa polypeptide present in all epithelial tissues and it is the prime mediator of cell-cell interactions. An immunohistochemical technique utilised the monoclonal antibody HECD-1 to evaluate E-cad expression in microwave treated, paraffin embedded sections from 120 patients. The phenotype of the specimens from the patients were metaplastic [41] and dysplastic mucosa [24], invasive squamous carcinoma [15] and adenocarcinoma [18] and corresponding metastatic lesions [10] as well as 12 specimens of normal oesophageal mucosae. Surface expression was high in non-metaplastic tissue and in non-dysplastic metaplasia but was reduced extensively in dysplasia. In addition in squamous carcinoma and adenocarcinoma E-cad was characteristically expressed in the cytoplasm and this was associated with poor morphological differentiation. SDS-PAGE gel protein analysis revealed the characteristic 120 kDa sized protein in normal squamous oesophageal tissue. In Barrett's metaplastic tissue and carcinoma, however, stronger bands at 108 kDa and 45 kDa were also present, suggesting either decreased glycosylation or a truncated protein in the metaplastic and neoplastic tissue, respectively. In conclusion changes in E-cad immunoreactivity and cellular localisation occur in premalignant metaplastic epithelium of the oesophagus. Further studies are in progress to evaluate whether the abnormal E-cad protein reflects both loss of function and may be used as a biomarker in pre-malignant lesions.
Collapse
Affiliation(s)
- J Jankowski
- ROYAL POSTGRAD MED SCH,DEPT HISTOL,CELL ADHES LAB,DU CANE RD,LONDON W12 0HS,ENGLAND. ROYAL POSTGRAD MED SCH,DEPT HISTOL,IMPERIAL CANC RES FUND LAB,GASTROINTESTINAL GENE GRP,LONDON W12 0HS,ENGLAND. KYOTO UNIV,DEPT BIOPHYS,KYOTO 606,JAPAN
| | | | | | | | | | | |
Collapse
|
26
|
Alcaraz L, Belda-Ferre P, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, Mira A. Identifying a healthy oral microbiome through metagenomics. Clin Microbiol Infect 2012; 18 Suppl 4:54-7. [DOI: 10.1111/j.1469-0691.2012.03857.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
27
|
Cirillo N, Hassona Y, Pignatelli M, Gasparoto T, Morgan D, Prime S. Characterization of a Novel Oral Glucocorticoid System and Its Possible Role in Disease. J Dent Res 2012; 91:97-103. [DOI: 10.1177/0022034511427909] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
Synthetic corticosteroids are used widely for the treatment of a variety of diseases of the mouth. However, little is known as to whether the oral mucosa is able to modulate the local concentration of active corticosteroids or to produce steroids de novo. This has important clinical implications, because tissue-specific regulation of glucocorticoids is a key determinant of the clinical efficacy of these drugs. In the present study, we show that oral fibroblasts and keratinocytes expressed ACTH receptor (MC2R), glucocorticoid receptor (GR), and 11β-hydroxysteroid dehydrogenases (11β-HSDs). Unlike keratinocytes, fibroblasts lacked 11β-HSD2 and could not effectively deactivate exogenously administered cortisol. However, both cell types were able not only to activate cortisone into the active form cortisol, but also to synthesize cortisol de novo following stimulation with ACTH. 11β-HSD2, the enzyme controlling cortisol deactivation, exhibited different patterns of expression in normal (squamous epithelium and salivary glands) and diseased oral mucosa (squamous cell carcinoma and mucoepidermoid carcinoma). Blocking of endogenous cortisol catabolism in keratinocytes with the 11β-HSD2 inhibitor 18β-glycyrrhetinic acid mimicked the effect of exogenous administration of hydrocortisone and partially prevented the detrimental effects induced by pemphigus vulgaris sera. Analysis of the data demonstrates that a novel, non-adrenal glucocorticoid system is present in the oral mucosa that may play an important role in disease.
Collapse
Affiliation(s)
- N. Cirillo
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS1 2LY, UK
| | - Y. Hassona
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS1 2LY, UK
| | - M. Pignatelli
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, UK
| | - T.H. Gasparoto
- Bauru School of Dentistry, University of São Paulo, Brazil
| | - D.J. Morgan
- School of Cellular & Molecular Medicine, University of Bristol, UK
| | - S.S. Prime
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS1 2LY, UK
| |
Collapse
|
28
|
Neef A, Latorre A, Peretó J, Silva FJ, Pignatelli M, Moya A. Genome economization in the endosymbiont of the wood roach Cryptocercus punctulatus due to drastic loss of amino acid synthesis capabilities. Genome Biol Evol 2011; 3:1437-48. [PMID: 22094859 PMCID: PMC3296467 DOI: 10.1093/gbe/evr118] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2011] [Indexed: 02/07/2023] Open
Abstract
Cockroaches (Blattaria: Dictyoptera) harbor the endosymbiont Blattabacterium sp. in their abdominal fat body. This endosymbiont is involved in nitrogen recycling and amino acid provision to its host. In this study, the genome of Blattabacterium sp. of Cryptocercus punctulatus (BCpu) was sequenced and compared with those of the symbionts of Blattella germanica and Periplaneta americana, BBge and BPam, respectively. The BCpu genome consists of a chromosome of 605.7 kb and a plasmid of 3.8 kb and is therefore approximately 31 kb smaller than the other two aforementioned genomes. The size reduction is due to the loss of 55 genes, 23 of which belong to biosynthetic pathways for amino acids. The pathways for the production of tryptophan, leucine, isoleucine/threonine/valine, methionine, and cysteine have been completely lost. Additionally, the genes for the enzymes catalyzing the last steps of arginine and lysine biosynthesis, argH and lysA, were found to be missing and pseudogenized, respectively. These gene losses render BCpu auxotrophic for nine amino acids more than those corresponding to BBge and BPam. BCpu has also lost capacities for sulfate reduction, production of heme groups, as well as genes for several other unlinked metabolic processes, and genes present in BBge and BPam in duplicates. Amino acids and cofactors that are not synthesized by BCpu are either produced in abundance by hindgut microbiota or are provisioned via a copious diet of dampwood colonized by putrefying microbiota, supplying host and Blattabacterium symbiont with the necessary nutrients and thus permitting genome economization of BCpu.
Collapse
Affiliation(s)
- Alexander Neef
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud—Centro Superior Investigación Salud Pública (Generalitat Valenciana)/Institut Cavanilles de Biodiversitat y Biologia Evolutiva, Universitat de València, Spain
- Departament de Genètica, Universitat de València, Spain
| | - Juli Peretó
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Spain
| | - Francisco J. Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud—Centro Superior Investigación Salud Pública (Generalitat Valenciana)/Institut Cavanilles de Biodiversitat y Biologia Evolutiva, Universitat de València, Spain
- Departament de Genètica, Universitat de València, Spain
| | - Miguel Pignatelli
- Unidad Mixta de Investigación en Genómica y Salud—Centro Superior Investigación Salud Pública (Generalitat Valenciana)/Institut Cavanilles de Biodiversitat y Biologia Evolutiva, Universitat de València, Spain
- Present address: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud—Centro Superior Investigación Salud Pública (Generalitat Valenciana)/Institut Cavanilles de Biodiversitat y Biologia Evolutiva, Universitat de València, Spain
- Departament de Genètica, Universitat de València, Spain
| |
Collapse
|
29
|
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GRS, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Harrow J, Herrero J, Hubbard TJP, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SMJ. Ensembl 2012. Nucleic Acids Res 2011; 40:D84-90. [PMID: 22086963 PMCID: PMC3245178 DOI: 10.1093/nar/gkr991] [Citation(s) in RCA: 806] [Impact Index Per Article: 62.0] [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: 12/19/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.
Collapse
Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Reimundo P, Pignatelli M, Alcaraz LD, D'Auria G, Moya A, Guijarro JA. Genome sequence of Lactococcus garvieae UNIUD074, isolated in Italy from a lactococcosis outbreak. J Bacteriol 2011; 193:3684-5. [PMID: 21602331 PMCID: PMC3133331 DOI: 10.1128/jb.05210-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Lactococcus garvieae is the etiological agent of lactococcosis disease, affecting many cultured fish species worldwide. In addition, this bacterium is currently considered a potential zoonotic microorganism since it is known to cause several opportunistic human infections. Here we present the draft genome sequence of the L. garvieae strain UNIUD074.
Collapse
Affiliation(s)
- Pilar Reimundo
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, IUBA, Universidad de Oviedo, 33006 Oviedo, Spain.
| | | | | | | | | | | |
Collapse
|
31
|
Hughes R, Cirillo N, Pignatelli M. Do the desmosomal cadherins have a role in the invasion and metastasis of oral squamous cell carcinoma? Br J Oral Maxillofac Surg 2011. [DOI: 10.1016/j.bjoms.2011.03.119] [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: 10/18/2022]
|
32
|
Abstract
A frequent step in metagenomic data analysis comprises the assembly of the sequenced reads. Many assembly tools have been published in the last years targeting data coming from next-generation sequencing (NGS) technologies but these assemblers have not been designed for or tested in multi-genome scenarios that characterize metagenomic studies. Here we provide a critical assessment of current de novo short reads assembly tools in multi-genome scenarios using complex simulated metagenomic data. With this approach we tested the fidelity of different assemblers in metagenomic studies demonstrating that even under the simplest compositions the number of chimeric contigs involving different species is noticeable. We further showed that the assembly process reduces the accuracy of the functional classification of the metagenomic data and that these errors can be overcome raising the coverage of the studied metagenome. The results presented here highlight the particular difficulties that de novo genome assemblers face in multi-genome scenarios demonstrating that these difficulties, that often compromise the functional classification of the analyzed data, can be overcome with a high sequencing effort.
Collapse
Affiliation(s)
- Miguel Pignatelli
- Unitat Mixta d'Investigació en Genòmica i Salut, Centre Superior d'Investigació en Salut Pública/UVEG-Institut Cavanilles, Valencia, Spain.
| | | |
Collapse
|
33
|
Gosalbes MJ, Durbán A, Pignatelli M, Abellan JJ, Jiménez-Hernández N, Pérez-Cobas AE, Latorre A, Moya A. Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One 2011; 6:e17447. [PMID: 21408168 PMCID: PMC3050895 DOI: 10.1371/journal.pone.0017447] [Citation(s) in RCA: 237] [Impact Index Per Article: 18.2] [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: 09/21/2010] [Accepted: 02/03/2011] [Indexed: 02/07/2023] Open
Abstract
The human gut is the natural habitat for a large and dynamic bacterial community that has a great relevance for health. Metagenomics is increasing our knowledge of gene content as well as of functional and genetic variability in this microbiome. However, little is known about the active bacteria and their function(s) in the gastrointestinal tract. We performed a metatranscriptomic study on ten healthy volunteers to elucidate the active members of the gut microbiome and their functionality under conditions of health. First, the microbial cDNAs obtained from each sample were sequenced using 454 technology. The analysis of 16S transcripts showed the phylogenetic structure of the active microbial community. Lachnospiraceae, Ruminococcaceae, Bacteroidaceae, Prevotellaceae, and Rickenellaceae were the predominant families detected in the active microbiota. The characterization of mRNAs revealed a uniform functional pattern in healthy individuals. The main functional roles of the gut microbiota were carbohydrate metabolism, energy production and synthesis of cellular components. In contrast, housekeeping activities such as amino acid and lipid metabolism were underrepresented in the metatranscriptome. Our results provide new insights into the functionality of the complex gut microbiota in healthy individuals. In this RNA-based survey, we also detected small RNAs, which are important regulatory elements in prokaryotic physiology and pathogenicity.
Collapse
Affiliation(s)
- María José Gosalbes
- Unidad Mixta de Investigación en Genómica y Salud-Centro Superior Investigación en Salud Pública (Generalitat Valenciana)/Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, València, Spain
| | - Ana Durbán
- Unidad Mixta de Investigación en Genómica y Salud-Centro Superior Investigación en Salud Pública (Generalitat Valenciana)/Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, València, Spain
| | - Miguel Pignatelli
- Unidad Mixta de Investigación en Genómica y Salud-Centro Superior Investigación en Salud Pública (Generalitat Valenciana)/Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, València, Spain
| | - Juan José Abellan
- Unidad Mixta de Investigación en Genómica y Salud-Centro Superior Investigación en Salud Pública (Generalitat Valenciana)/Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, València, Spain
| | - Nuria Jiménez-Hernández
- Unidad Mixta de Investigación en Genómica y Salud-Centro Superior Investigación en Salud Pública (Generalitat Valenciana)/Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, València, Spain
| | - Ana Elena Pérez-Cobas
- Unidad Mixta de Investigación en Genómica y Salud-Centro Superior Investigación en Salud Pública (Generalitat Valenciana)/Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
| | - Amparo Latorre
- Unidad Mixta de Investigación en Genómica y Salud-Centro Superior Investigación en Salud Pública (Generalitat Valenciana)/Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, València, Spain
| | - Andrés Moya
- Unidad Mixta de Investigación en Genómica y Salud-Centro Superior Investigación en Salud Pública (Generalitat Valenciana)/Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universitat de València), València, Spain
- CIBER en Epidemiología y Salud Pública, València, Spain
- * E-mail:
| |
Collapse
|
34
|
Talarico G, Piscopo P, Gasparini M, Salati E, Pignatelli M, Pietracupa S, Malvezzi-Campeggi L, Crestini A, Boschi S, Lenzi GL, Confaloni A, Bruno G. The London APP mutation (Val717Ile) associated with early shifting abilities and behavioral changes in two Italian families with early-onset Alzheimer's disease. Dement Geriatr Cogn Disord 2010; 29:484-90. [PMID: 20523046 DOI: 10.1159/000313541] [Citation(s) in RCA: 11] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/11/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Mutations in the amyloid precursor protein gene were the first to be recognized as a cause of Alzheimer's disease (AD). METHODS We describe 2 Italian families showing the missense mutation in exon 17 of the amyloid precursor protein gene on chromosome 21 (Val717Ile), known as London mutation. RESULTS In 1 family, this mutation was responsible for AD in 3 out of 7 siblings and it is also present in a fourth sibling who has only shown signs of executive dysfunction so far. Two subjects of the other family with AD diagnosis were carriers of the same mutation. CONCLUSION All AD subjects showed a cognitive profile characterized by early impairment in long-term memory, shifting abilities and affective symptoms beginning in the fifth decade of life.
Collapse
Affiliation(s)
- G Talarico
- Department of Neurological Science, Memory Clinic, University Sapienza, Rome, Italy.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Matrisciano F, Nasca C, Molinaro G, Riozzi B, Scaccianoce S, Raggi MA, Mercolini L, Biagioni F, Mathè AA, Sanna E, Maciocco E, Pignatelli M, Biggio G, Nicoletti F. Enhanced expression of the neuronal K+/Cl- cotransporter, KCC2, in spontaneously depressed Flinders Sensitive Line rats. Brain Res 2010; 1325:112-20. [PMID: 20153734 DOI: 10.1016/j.brainres.2010.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [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: 01/08/2010] [Revised: 02/02/2010] [Accepted: 02/04/2010] [Indexed: 11/17/2022]
Abstract
We used Flinder Sensitive Line (FSL) rats, a genetic model of unipolar depression, to examine whether changes in central GABAergic transmission are associated with a depressed phenotype. FSL rats showed an increased behavioral response to low doses of diazepam, as compared to either Sprague Dawley (SD) or Flinder Resistant Line (FRL) rats used as controls. Diazepam at a dose of 0.3 mg/kg, i.p., induced a robust impairment of motor coordination in FSL rats, but was virtually inactive in SD or FRL rats. The increased responsiveness of FSL rats was not due to changes in the brain levels of diazepam or its active metabolites, or to increases in the number or affinity of benzodiazepine recognition sites, as shown by the analysis of [(3)H]-flunitrazepam binding in the hippocampus, cerebral cortex or cerebellum. We therefore examined whether FSL rats differed from control rats for the expression levels of the K(+)/Cl(-) cotransporter, KCC2, which transports Cl(-) ions out of neurons, thus creating the concentration gradient that allows Cl(-) influx through the anion channel associated with GABA(A) receptors. Combined immunoblot and immunohistochemical data showed a widespread increase in KCC2 expression in FSL rats, as compared with control rats. The increase was more prominent in the cerebellum, where KCC2 was largely expressed in the granular layer. These data raise the interesting possibility that a spontaneous depressive state in animals is associated with an amplified GABAergic transmission in the CNS resulting from an enhanced expression of KCC2.
Collapse
Affiliation(s)
- F Matrisciano
- Department of Physiology and Pharmacology, Sant'Andrea Hospital, University of Rome Sapienza, Rome, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
BACKGROUND The increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa. RESULTS We used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB. CONCLUSIONS This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina.
Collapse
Affiliation(s)
- Javier Tamames
- Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP) y Universidad de Valencia (Instituto Cavanilles de Biodiversidad y Biología Evolutiva). Avenida de Cataluña 21, 46020 Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
- Centro Nacional de Biotecnología (CNB-CSIC). C/Darwin 3, 28049 Madrid, Spain
| | - Juan José Abellán
- Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP) y Universidad de Valencia (Instituto Cavanilles de Biodiversidad y Biología Evolutiva). Avenida de Cataluña 21, 46020 Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Miguel Pignatelli
- Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP) y Universidad de Valencia (Instituto Cavanilles de Biodiversidad y Biología Evolutiva). Avenida de Cataluña 21, 46020 Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Antonio Camacho
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva y Departamento de Microbiología y Ecología Universidad de Valencia. C/Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Andrés Moya
- Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP) y Universidad de Valencia (Instituto Cavanilles de Biodiversidad y Biología Evolutiva). Avenida de Cataluña 21, 46020 Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| |
Collapse
|
37
|
Huerta-Cepas J, Marcet-Houben M, Pignatelli M, Moya A, Gabaldón T. The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes. Insect Mol Biol 2010; 19 Suppl 2:13-21. [PMID: 20482636 DOI: 10.1111/j.1365-2583.2009.00947.x] [Citation(s) in RCA: 28] [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] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Phylogenetic analyses serve many purposes, including the establishment of orthology relationships, the prediction of protein function and the detection of important evolutionary events. Within the context of the sequencing of the genome of the pea aphid, Acyrthosiphon pisum, we undertook a phylogenetic analysis for every protein of this species. The resulting phylome includes the evolutionary relationships of all predicted aphid proteins and their homologues among 13 other fully-sequenced arthropods and three out-group species. Subsequent analyses have revealed multiple gene expansions that are specific to aphids and have served to transfer functional annotations to 4058 pea aphid genes that display one-to-one orthology relationships with Drosophila melanogaster annotated genes. All phylogenies and alignments are accessible through the PhylomeDB database. Here we provide a description of this dataset and provide some examples on how can it be exploited.
Collapse
|
38
|
Gerardo NM, Altincicek B, Anselme C, Atamian H, Barribeau SM, de Vos M, Duncan EJ, Evans JD, Gabaldón T, Ghanim M, Heddi A, Kaloshian I, Latorre A, Moya A, Nakabachi A, Parker BJ, Pérez-Brocal V, Pignatelli M, Rahbé Y, Ramsey JS, Spragg CJ, Tamames J, Tamarit D, Tamborindeguy C, Vincent-Monegat C, Vilcinskas A. Immunity and other defenses in pea aphids, Acyrthosiphon pisum. Genome Biol 2010; 11:R21. [PMID: 20178569 PMCID: PMC2872881 DOI: 10.1186/gb-2010-11-2-r21] [Citation(s) in RCA: 304] [Impact Index Per Article: 21.7] [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: 08/22/2009] [Revised: 10/07/2009] [Accepted: 02/23/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Recent genomic analyses of arthropod defense mechanisms suggest conservation of key elements underlying responses to pathogens, parasites and stresses. At the center of pathogen-induced immune responses are signaling pathways triggered by the recognition of fungal, bacterial and viral signatures. These pathways result in the production of response molecules, such as antimicrobial peptides and lysozymes, which degrade or destroy invaders. Using the recently sequenced genome of the pea aphid (Acyrthosiphon pisum), we conducted the first extensive annotation of the immune and stress gene repertoire of a hemipterous insect, which is phylogenetically distantly related to previously characterized insects models. RESULTS Strikingly, pea aphids appear to be missing genes present in insect genomes characterized to date and thought critical for recognition, signaling and killing of microbes. In line with results of gene annotation, experimental analyses designed to characterize immune response through the isolation of RNA transcripts and proteins from immune-challenged pea aphids uncovered few immune-related products. Gene expression studies, however, indicated some expression of immune and stress-related genes. CONCLUSIONS The absence of genes suspected to be essential for the insect immune response suggests that the traditional view of insect immunity may not be as broadly applicable as once thought. The limitations of the aphid immune system may be representative of a broad range of insects, or may be aphid specific. We suggest that several aspects of the aphid life style, such as their association with microbial symbionts, could facilitate survival without strong immune protection.
Collapse
Affiliation(s)
- Nicole M Gerardo
- Department of Biology, Emory University, O Wayne Rollins Research Center, 1510 E. Clifton Road NE, Atlanta, GA, 30322, USA
| | - Boran Altincicek
- Interdisciplinary Research Center, Institute of Phytopathology and Applied Zoology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Caroline Anselme
- Université de Lyon, INRA, INSA-Lyon, IFR41 BioEnvironnement et Santé, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Bat. Louis-Pasteur 20 ave Albert-Einstein, F-69621 Villeurbanne, France
- UMR Interactions Biotiques et Santé Végétale, INRA 1301-CNRS 6243-Université de Nice-Sophia Antipolis, 400 routes des Chappe, F-06903 Sophia-Antipolis cedex, France
| | - Hagop Atamian
- Department of Nematology, Graduate Program in Genetics, Genomics and Bioinformatics, University of California, 900 University Ave, Riverside, CA 92521, USA
| | - Seth M Barribeau
- Department of Biology, Emory University, O Wayne Rollins Research Center, 1510 E. Clifton Road NE, Atlanta, GA, 30322, USA
| | - Martin de Vos
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Elizabeth J Duncan
- Genetics Otago and The Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, Box 56, Dunedin 9054, New Zealand
| | - Jay D Evans
- USDA-ARS Bee Research Lab, BARC-East Bldg 476, Beltsville, MD 20705, USA
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Murad Ghanim
- Department of Entomology, The Volcani Center, Bet Dagan 50250, Israel
| | - Adelaziz Heddi
- Université de Lyon, INRA, INSA-Lyon, IFR41 BioEnvironnement et Santé, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Bat. Louis-Pasteur 20 ave Albert-Einstein, F-69621 Villeurbanne, France
| | - Isgouhi Kaloshian
- Department of Nematology, Graduate Program in Genetics, Genomics and Bioinformatics, University of California, 900 University Ave, Riverside, CA 92521, USA
| | - Amparo Latorre
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Avenida Blasco Ibañez 13, 46071 València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp) and Centro Superior de Investigación en Salud Pública (CSISP), Conselleria de Sanidad (Generalitat Valenciana), Avenida de Cataluña 21, 46020 València, Spain
| | - Andres Moya
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Avenida Blasco Ibañez 13, 46071 València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp) and Centro Superior de Investigación en Salud Pública (CSISP), Conselleria de Sanidad (Generalitat Valenciana), Avenida de Cataluña 21, 46020 València, Spain
| | - Atsushi Nakabachi
- Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Benjamin J Parker
- Department of Biology, Emory University, O Wayne Rollins Research Center, 1510 E. Clifton Road NE, Atlanta, GA, 30322, USA
| | - Vincente Pérez-Brocal
- Université de Lyon, INRA, INSA-Lyon, IFR41 BioEnvironnement et Santé, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Bat. Louis-Pasteur 20 ave Albert-Einstein, F-69621 Villeurbanne, France
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Avenida Blasco Ibañez 13, 46071 València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp) and Centro Superior de Investigación en Salud Pública (CSISP), Conselleria de Sanidad (Generalitat Valenciana), Avenida de Cataluña 21, 46020 València, Spain
| | - Miguel Pignatelli
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Avenida Blasco Ibañez 13, 46071 València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp) and Centro Superior de Investigación en Salud Pública (CSISP), Conselleria de Sanidad (Generalitat Valenciana), Avenida de Cataluña 21, 46020 València, Spain
| | - Yvan Rahbé
- Université de Lyon, INRA, INSA-Lyon, IFR41 BioEnvironnement et Santé, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Bat. Louis-Pasteur 20 ave Albert-Einstein, F-69621 Villeurbanne, France
| | - John S Ramsey
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Chelsea J Spragg
- Department of Biology, Emory University, O Wayne Rollins Research Center, 1510 E. Clifton Road NE, Atlanta, GA, 30322, USA
| | - Javier Tamames
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Avenida Blasco Ibañez 13, 46071 València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp) and Centro Superior de Investigación en Salud Pública (CSISP), Conselleria de Sanidad (Generalitat Valenciana), Avenida de Cataluña 21, 46020 València, Spain
| | - Daniel Tamarit
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Avenida Blasco Ibañez 13, 46071 València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp) and Centro Superior de Investigación en Salud Pública (CSISP), Conselleria de Sanidad (Generalitat Valenciana), Avenida de Cataluña 21, 46020 València, Spain
| | - Cecilia Tamborindeguy
- Plant Pathology and Plant-Microbe Biology Department, Cornell University, Tower Road, Ithaca, NY 14853, USA
- Department of Entomology, Texas A&M, College Station, TX 77843-2475, USA
| | - Caroline Vincent-Monegat
- Université de Lyon, INRA, INSA-Lyon, IFR41 BioEnvironnement et Santé, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Bat. Louis-Pasteur 20 ave Albert-Einstein, F-69621 Villeurbanne, France
| | - Andreas Vilcinskas
- Interdisciplinary Research Center, Institute of Phytopathology and Applied Zoology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| |
Collapse
|
39
|
López-Sánchez MJ, Neef A, Peretó J, Patiño-Navarrete R, Pignatelli M, Latorre A, Moya A. Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica. PLoS Genet 2009; 5:e1000721. [PMID: 19911043 PMCID: PMC2768785 DOI: 10.1371/journal.pgen.1000721] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [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: 07/31/2009] [Accepted: 10/15/2009] [Indexed: 02/07/2023] Open
Abstract
Bacterial endosymbionts of insects play a central role in upgrading the diet of their hosts. In certain cases, such as aphids and tsetse flies, endosymbionts complement the metabolic capacity of hosts living on nutrient-deficient diets, while the bacteria harbored by omnivorous carpenter ants are involved in nitrogen recycling. In this study, we describe the genome sequence and inferred metabolism of Blattabacterium strain Bge, the primary Flavobacteria endosymbiont of the omnivorous German cockroach Blattella germanica. Through comparative genomics with other insect endosymbionts and free-living Flavobacteria we reveal that Blattabacterium strain Bge shares the same distribution of functional gene categories only with Blochmannia strains, the primary Gamma-Proteobacteria endosymbiont of carpenter ants. This is a remarkable example of evolutionary convergence during the symbiotic process, involving very distant phylogenetic bacterial taxa within hosts feeding on similar diets. Despite this similarity, different nitrogen economy strategies have emerged in each case. Both bacterial endosymbionts code for urease but display different metabolic functions: Blochmannia strains produce ammonia from dietary urea and then use it as a source of nitrogen, whereas Blattabacterium strain Bge codes for the complete urea cycle that, in combination with urease, produces ammonia as an end product. Not only does the cockroach endosymbiont play an essential role in nutrient supply to the host, but also in the catabolic use of amino acids and nitrogen excretion, as strongly suggested by the stoichiometric analysis of the inferred metabolic network. Here, we explain the metabolic reasons underlying the enigmatic return of cockroaches to the ancestral ammonotelic state.
Collapse
Affiliation(s)
- Maria J. López-Sánchez
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Alexander Neef
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Barcelona, Spain
| | - Juli Peretó
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, València, Spain
| | - Rafael Patiño-Navarrete
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Miguel Pignatelli
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Barcelona, Spain
- Centro Superior de Investigación en Salud Pública (CSISP), València, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Barcelona, Spain
- Centro Superior de Investigación en Salud Pública (CSISP), València, Spain
- Departament de Genètica, Universitat de València, València, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Barcelona, Spain
- Centro Superior de Investigación en Salud Pública (CSISP), València, Spain
- Departament de Genètica, Universitat de València, València, Spain
- * E-mail:
| |
Collapse
|
40
|
Qualtrough D, Singh K, Banu N, Paraskeva C, Pignatelli M. The actin-bundling protein fascin is overexpressed in colorectal adenomas and promotes motility in adenoma cells in vitro. Br J Cancer 2009; 101:1124-9. [PMID: 19738613 PMCID: PMC2768091 DOI: 10.1038/sj.bjc.6605286] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [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: 12/02/2022] Open
Abstract
Background: Fascin is overexpressed in many cancers, including colorectal, but its role in the malignant transformation of benign colorectal adenomas is unclear. Methods: Immunohistochemical analysis of fascin expression was carried out in resected human colorectal adenoma specimens. The effects of forced overexpression of fascin on adenoma cell motility were also analysed. Results: We show fascin overexpression in adenomas increasing with tumour size, histological type, and degree of dysplasia and increased cell motility in adenoma cell lines following fascin transfection. Conclusion: These data suggest an important role for fascin in the malignant progression of colorectal tumours.
Collapse
Affiliation(s)
- D Qualtrough
- Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK.
| | | | | | | | | |
Collapse
|
41
|
Abstract
SUMMARY There is increasing evidence showing that co-expression of genes that cluster along the genome is a common characteristic of eukaryotic transcriptomes. Several algorithms have been used to date in the identification of these kinds of gene organization. Here, we present a web tool called CROC that aims to help in the identification and analysis of genomic gene clusters. This method has been successfully used before in the identification of chromosomal clusters in different eukaryotic species. AVAILABILITY The web server is freely available to non-commercial users at the following address: http://metagenomics.uv.es/CROC/.
Collapse
Affiliation(s)
- Miguel Pignatelli
- Instituto Cavanilles of Biodiversity and Evolutionary Biology, University of Valencia, Apdo, Valencia, Spain.
| | | | | | | | | |
Collapse
|
42
|
Servitja JM, Pignatelli M, Maestro MA, Cardalda C, Boj SF, Lozano J, Blanco E, Lafuente A, McCarthy MI, Sumoy L, Guigó R, Ferrer J. Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver. Mol Cell Biol 2009; 29:2945-59. [PMID: 19289501 PMCID: PMC2682018 DOI: 10.1128/mcb.01389-08] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [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: 09/03/2008] [Revised: 10/29/2008] [Accepted: 03/02/2009] [Indexed: 01/08/2023] Open
Abstract
Heterozygous HNF1A mutations cause pancreatic-islet beta-cell dysfunction and monogenic diabetes (MODY3). Hnf1alpha is known to regulate numerous hepatic genes, yet knowledge of its function in pancreatic islets is more limited. We now show that Hnf1a deficiency in mice leads to highly tissue-specific changes in the expression of genes involved in key functions of both islets and liver. To gain insights into the mechanisms of tissue-specific Hnf1alpha regulation, we integrated expression studies of Hnf1a-deficient mice with identification of direct Hnf1alpha targets. We demonstrate that Hnf1alpha can bind in a tissue-selective manner to genes that are expressed only in liver or islets. We also show that Hnf1alpha is essential only for the transcription of a minor fraction of its direct-target genes. Even among genes that were expressed in both liver and islets, the subset of targets showing functional dependence on Hnf1alpha was highly tissue specific. This was partly explained by the compensatory occupancy by the paralog Hnf1beta at selected genes in Hnf1a-deficient liver. In keeping with these findings, the biological consequences of Hnf1a deficiency were markedly different in islets and liver. Notably, Hnf1a deficiency led to impaired large-T-antigen-induced growth and oncogenesis in beta cells yet enhanced proliferation in hepatocytes. Collectively, these findings show that Hnf1alpha governs broad, highly tissue-specific genetic programs in pancreatic islets and liver and reveal key consequences of Hnf1a deficiency relevant to the pathophysiology of monogenic diabetes.
Collapse
Affiliation(s)
- Joan-Marc Servitja
- Genomic Programming of Beta-Cells Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
EnvDB is a database that classifies the environmental samples and their associated 16S rDNA sequences currently stored in GenBank. The samples were categorized in a three-level, hierarchical classification of media: the five upper levels (terrestrial, aquatic, thermal, host-associated and other) are further decomposed in 20 intermediate (such as marine, marine sediments, freshwater, soil, gut, etc.) and 47 lower levels (for instance, soil is further decomposed in forest, agricultural, wetlands, grasslands, tropical, arid, etc.). Each sample was also characterized with nine environmental features: polluted, diseased (for clinical samples), acidic, alkaline, hot environment, cold environment, saline, anoxic and restricted (when the study is focused only in particular taxonomic groups). The classification of samples was aided by text-mining techniques, complemented with careful curation and completion by human experts. EnvDB currently includes 359 928 sequences from 3502 samples. The sequences were clustered at several identity levels to obtain operative taxonomic units (OTUs). Sequences and OTUs have been taxonomically assigned to the maximum possible resolution by different procedures. The user can obtain information about sequences, OTUs, samples and environments, combining these tables using a flexible querying system that allows generating very diverse queries. Thus, the user can easily inspect the presence and abundance of particular taxa in particular samples and environments. The database also allows the users to run analyses with their own data: users can input their sequences and find the closest sequences or samples in the database. EnvDB can be accessed in the web address http://metagenomics.uv.es/envDB.
Collapse
Affiliation(s)
- Miguel Pignatelli
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Polígono La Coma s/n, 46980 Paterna (Valencia), Spain. Centro Superior de Investigación en Salud Pública (CSISP), Dirección General de Salud Pública, C/San Vicente 83, 46007 Valencia, Spain. CIBER en Epidemiología y Salud Pública (CIBER-ESP), Spain
| | | | | |
Collapse
|
44
|
Abstract
Contact: Javier.tamames@uv.es
Collapse
|
45
|
Blanco E, Pignatelli M, Beltran S, Punset A, Pérez-Lluch S, Serras F, Guigó R, Corominas M. Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila. Genome Biol 2008; 9:R134. [PMID: 18783608 PMCID: PMC2592712 DOI: 10.1186/gb-2008-9-9-r134] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [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: 08/01/2008] [Revised: 09/04/2008] [Accepted: 09/10/2008] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The trithorax group (trxG) and Polycomb group (PcG) proteins are responsible for the maintenance of stable transcriptional patterns of many developmental regulators. They bind to specific regions of DNA and direct the post-translational modifications of histones, playing a role in the dynamics of chromatin structure. RESULTS We have performed genome-wide expression studies of trx and ash2 mutants in Drosophila melanogaster. Using computational analysis of our microarray data, we have identified 25 clusters of genes potentially regulated by TRX. Most of these clusters consist of genes that encode structural proteins involved in cuticle formation. This organization appears to be a distinctive feature of the regulatory networks of TRX and other chromatin regulators, since we have observed the same arrangement in clusters after experiments performed with ASH2, as well as in experiments performed by others with NURF, dMyc, and ASH1. We have also found many of these clusters to be significantly conserved in D. simulans, D. yakuba, D. pseudoobscura and partially in Anopheles gambiae. CONCLUSION The analysis of genes governed by chromatin regulators has led to the identification of clusters of functionally related genes conserved in other insect species, suggesting this chromosomal organization is biologically important. Moreover, our results indicate that TRX and other chromatin regulators may act globally on chromatin domains that contain transcriptionally co-regulated genes.
Collapse
Affiliation(s)
- Enrique Blanco
- Departament de Genètica and Institut de Biomedicina de la Universitat de Barcelona, Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Beltran S, Angulo M, Pignatelli M, Serras F, Corominas M. Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions. Genome Biol 2007; 8:R67. [PMID: 17466076 PMCID: PMC1896016 DOI: 10.1186/gb-2007-8-4-r67] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [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: 12/04/2006] [Revised: 03/05/2007] [Accepted: 04/28/2007] [Indexed: 12/16/2022] Open
Abstract
Analysis of the gene expression profiles of wing imaginal discs from ash2 and ash1 mutants shows that they are highly similar, supporting a model in which they act together to maintain stable states of transcription. Background The trithorax group (trxG) genes absent, small or homeotic discs 1 (ash1) and 2 (ash2) were isolated in a screen for mutants with abnormal imaginal discs. Mutations in either gene cause homeotic transformations but Hox genes are not their only targets. Although analysis of double mutants revealed that ash2 and ash1 mutations enhance each other's phenotypes, suggesting they are functionally related, it was shown that these proteins are subunits of distinct complexes. Results The analysis of wing imaginal disc transcriptomes from ash2 and ash1 mutants showed that they are highly similar. Functional annotation of regulated genes using Gene Ontology allowed identification of severely affected groups of genes that could be correlated to the wing phenotypes observed. Comparison of the differentially expressed genes with those from other genome-wide analyses revealed similarities between ASH2 and Sin3A, suggesting a putative functional relationship. Coimmunoprecipitation studies and immunolocalization on polytene chromosomes demonstrated that ASH2 and Sin3A interact with HCF (host-cell factor). The results of nucleosome western blots and clonal analysis indicated that ASH2 is necessary for trimethylation of the Lys4 on histone 3 (H3K4). Conclusion The similarity between the transcriptomes of ash2 and ash1 mutants supports a model in which the two genes act together to maintain stable states of transcription. Like in humans, both ASH2 and Sin3A bind HCF. Finally, the reduction of H3K4 trimethylation in ash2 mutants is the first evidence in Drosophila regarding the molecular function of this trxG gene.
Collapse
Affiliation(s)
- Sergi Beltran
- Departament de Genètica, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Mireia Angulo
- Departament de Genètica, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Miguel Pignatelli
- Departament de Genètica, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Florenci Serras
- Departament de Genètica, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Montserrat Corominas
- Departament de Genètica, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
| |
Collapse
|
47
|
Banu N, Buda A, Chell S, Elder D, Moorghen M, Paraskeva C, Qualtrough D, Pignatelli M. Inhibition of COX-2 with NS-398 decreases colon cancer cell motility through blocking epidermal growth factor receptor transactivation: possibilities for combination therapy. Cell Prolif 2007; 40:768-79. [PMID: 17877615 PMCID: PMC6496834 DOI: 10.1111/j.1365-2184.2007.00459.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED The use of non-steroidal anti-inflammatory drugs has proved of great interest in the prevention and treatment of colorectal cancer, although their precise mechanisms of action remain unclear. Overexpression of cyclooxygenase-2 (COX-2) and subsequent prostaglandin production promote metastasis and have been shown to increase cell motility in vitro. OBJECTIVE We have aimed to elucidate whether specific inhibition of COX-2 with NS-398 (NS-398 is a selective inhibitor of COX-2) would be able to inhibit motility of colorectal cancer cells and whether this was modulated through epidermal growth factor receptor (EGFR) transactivation. MATERIALS AND METHODS A transwell filter assay was used to study cell motility. Expression of COX-2, EGFR phosphorylation and prostaglandin E(2) (PGE(2)) receptors were assessed by Western blot analysis and reverse transcriptase-polymerase chain reaction. PGE(2) concentrations after NS-398 treatment were estimated by enzyme immunoassay. RESULTS Treatment with NS-398 significantly reduced PGE(2) levels and reduced cell migration in the HT29 and HCA7 colorectal carcinoma cell lines and this effect was rescued by addition of PGE(2). Furthermore, specific inhibition of COX-2 with NS-398 reduced EGFR phosphorylation in colorectal cancer cells. Direct inhibition of EGFR activity with AG1478 reduced PGE(2)-stimulated motility, clearly demonstrating that PGE(2 )acts via the EGFR-signalling pathway. The novel combination of NS-398 and AG1478 dramatically reduced migration of colorectal cancer cells. CONCLUSION The data presented indicate that the use of NS-398 in chemoprevention and adjuvant therapy for colorectal cancer may work in part, through the inhibition of cell motility. Furthermore, our data suggest that the combined use of non-steroidal anti-inflammatory drugs with EGFR antagonists could be explored further for future use in the clinic.
Collapse
Affiliation(s)
- N Banu
- Division of Histopathology, Department of Cellular and Molecular Medicine, School of Medical Sciences and Bristol Royal Infirmary, University of Bristol, Bristol, UK
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Ruocco LA, Viggiano D, Pignatelli M, Iannaccone T, Rimoli MG, Melisi D, Curcio A, De Lucia S, Carboni E, Gironi Carnevale UA, de Caprariis P, Sadile AG. Galactosilated dopamine increases attention without reducing activity in C57BL/6 mice. Behav Brain Res 2007; 187:449-54. [PMID: 18063140 DOI: 10.1016/j.bbr.2007.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [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: 10/03/2007] [Accepted: 10/08/2007] [Indexed: 11/17/2022]
Abstract
Different strategies can be used to carry dopamine into the brain such as L-Dopa precursors or galactosilated form of DA (GAL-DA). The aim of this study was to investigate whether GAL-DA would reduce hyperactivity and increase non-selective attention (NSA) in a mouse model of attention deficit hyperactivity disorder (ADHD), as, i.e. C57BL/6 as did in NHE rats. Here we report that GAL-DA increases NSA in a spatial novelty in C57BL/6 mice. They received a single i.p. injection of GAL-DA (10 mg/kg or 100 mg/kg) or equimolar galactose vehicle. Another mouse strain the Swiss albino was introduced as inbred control group. Three hours after last injection mice were tested in a Làt-maze for 30-min. Behaviour was analyzed for horizontal (traveled distance) and vertical activity (orienting frequency and scanning durations) which shares cognitive and non-cognitive nature, respectively. Ten milligram per kilograms of GAL-DA, increases scanning duration in C57BL/6 mice. Thus a low dose of GAL-DA increases NSA without reducing hyperactivity in this mouse model of ADHD.
Collapse
Affiliation(s)
- L A Ruocco
- Department of Experimental Medicine, II University of Naples, Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Gill GA, Buda A, Moorghen M, Dettmar PW, Pignatelli M. Characterisation of adherens and tight junctional molecules in normal animal larynx; determining a suitable model for studying molecular abnormalities in human laryngopharyngeal reflux. J Clin Pathol 2005; 58:1265-70. [PMID: 16311345 PMCID: PMC1770809 DOI: 10.1136/jcp.2004.016972] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2004] [Indexed: 11/04/2022]
Abstract
BACKGROUND The disruption of intercellular junctions in the larynx is a pathological feature of laryngopharyngeal reflux (LPR). Good experimental models are necessary to gain greater insight into the molecular mechanisms and alterations that result from abnormal exposure of the laryngeal epithelium to acid refluxate. AIMS To characterise laryngeal tissues from different species to determine the most suitable for use in experimental studies of LPR. METHODS Human and non-human laryngeal tissues (mouse, rat, guinea pig, porcine, and rabbit) were studied. Histological characterisation was performed by light microscopy. The expression and subcellular localisation of adherens junctional molecules (E-cadherin and beta catenin) was evaluated by immunohistochemistry, and tight junction molecules (occludin and zonula occludens 1 (ZO-1)) by western blotting. The ultrastructural features of porcine and human tissue were assessed by electron microscopy. RESULTS Porcine tissue revealed both respiratory-type and stratified squamous epithelium, as seen in the human larynx. The expression and subcellular localisation of the E-cadherin-catenin complex was detected in all species except mouse and rat. The pattern of ZO-1 and occludin expression was preserved in all species. CONCLUSION The expression of intercellular junctional complexes in porcine epithelium is similar to that seen in humans. These results confirm the suitability of these species to study molecular mechanisms of LPR in an experimental system.
Collapse
Affiliation(s)
- G A Gill
- Division of Histopathology, Department of Pathology and Microbiology, School of Medical Sciences and Bristol Royal Infirmary, University of Bristol, Bristol BS2 8HW, UK
| | | | | | | | | |
Collapse
|
50
|
Vestey SB, Sen C, Calder CJ, Perks CM, Pignatelli M, Winters ZE. Activated Akt expression in breast cancer: Correlation with p53, Hdm2 and patient outcome. Eur J Cancer 2005; 41:1017-25. [PMID: 15862750 DOI: 10.1016/j.ejca.2005.02.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [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: 10/27/2004] [Revised: 01/20/2005] [Accepted: 02/03/2005] [Indexed: 10/25/2022]
Abstract
Activation of protein kinase-B/Akt (pAkt) is mediated by oestrogen and involves HER-2 in vitro, to phosphorylate Hdm2 and influence p53 cytoplasmic localisation and degradation. Expression of all active Akt isoforms (pAkt) were examined, together with p53/Hdm2 subcellular expression in invasive ductal breast cancers (IDCs), to evaluate whether in vitro findings were related to clinical data and determine the effect on outcome. Immunohistochemical expression of serine 473 specific phosphorylated Akt (pAkt) isoforms (Akt-1,2,3) was evaluated in 97 patients, together with subcellular expression of p53/Hdm2. The results show that pAkt was evaluable in 95 patients with cytoplasmic expression in 81% and more likely to be associated with larger tumours (P=0.007), with no correlation with HER-2 expression. pAkt correlated with increasing levels of cytoplasmic p53 (P=0.025) and was associated with a reduced disease-free survival (P=0.04; univariate). In conclusion, pAkt has implications in breast cancer growth through mechanisms inactivating p53 with an association with immunohistochemical p53 expression, which is preferentially cytoplasmic. Despite in vitro associations, pAkt appears to be a variable marker of HER-2 expression.
Collapse
Affiliation(s)
- S B Vestey
- University of Bristol, Department of Clinical Sciences at South Bristol--Surgery, Level 7, Bristol Royal Infirmary, Marlborough Street, Bristol BS2 8HW, UK
| | | | | | | | | | | |
Collapse
|