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Abstract
Summary: The increasing size and complexity of biological databases has led to a growing trend to federate rather than duplicate them. In order to share data between federated databases, protocols for the exchange mechanism must be developed. One such data exchange protocol that is widely used is the Distributed Annotation System (DAS). For example, DAS has enabled small experimental groups to integrate their data into the Ensembl genome browser. We have developed ProServer, a simple, lightweight, Perl-based DAS server that does not depend on a separate HTTP server. The ProServer package is easily extensible, allowing data to be served from almost any underlying data model. Recent additions to the DAS protocol have enabled both structure and alignment (sequence and structural) data to be exchanged. ProServer allows both of these data types to be served. Availability: ProServer can be downloaded from http://www.sanger.ac.uk/proserver/ or CPAN http://search.cpan.org/~rpettett/. Details on the system requirements and installation of ProServer can be found at http://www.sanger.ac.uk/proserver/. Contact:rmp@sanger.ac.uk Supplementary Materials: DasClientExamples.pdf
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Affiliation(s)
- Robert D Finn
- Wellcome Trust Sanger Institute, Wellcome Trust Geome Campus, Hinxton, Cambridge, UK
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2
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Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, Haefliger C, Horton R, Howe K, Jackson DK, Kunde J, Koenig C, Liddle J, Niblett D, Otto T, Pettett R, Seemann S, Thompson C, West T, Rogers J, Olek A, Berlin K, Beck S. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 2006; 38:1378-85. [PMID: 17072317 PMCID: PMC3082778 DOI: 10.1038/ng1909] [Citation(s) in RCA: 933] [Impact Index Per Article: 51.8] [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: 04/26/2006] [Accepted: 09/18/2006] [Indexed: 12/17/2022]
Abstract
DNA methylation is the most stable type of epigenetic modification modulating the transcriptional plasticity of mammalian genomes. Using bisulfite DNA sequencing, we report high-resolution methylation profiles of human chromosomes 6, 20 and 22, providing a resource of about 1.9 million CpG methylation values derived from 12 different tissues. Analysis of six annotation categories showed that evolutionarily conserved regions are the predominant sites for differential DNA methylation and that a core region surrounding the transcriptional start site is an informative surrogate for promoter methylation. We find that 17% of the 873 analyzed genes are differentially methylated in their 5' UTRs and that about one-third of the differentially methylated 5' UTRs are inversely correlated with transcription. Despite the fact that our study controlled for factors reported to affect DNA methylation such as sex and age, we did not find any significant attributable effects. Our data suggest DNA methylation to be ontogenetically more stable than previously thought.
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MESH Headings
- 5' Untranslated Regions
- Adult
- Age Factors
- Aged
- Animals
- Chromosomes, Human, Pair 20/genetics
- Chromosomes, Human, Pair 20/metabolism
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 22/metabolism
- Chromosomes, Human, Pair 6/genetics
- Chromosomes, Human, Pair 6/metabolism
- CpG Islands
- DNA Methylation
- Epigenesis, Genetic
- Evolution, Molecular
- Female
- Humans
- Male
- Mice
- Middle Aged
- Organ Specificity
- Promoter Regions, Genetic
- Sex Characteristics
- Species Specificity
- Transcription, Genetic
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Affiliation(s)
- Florian Eckhardt
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Joern Lewin
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Rene Cortese
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Vardhman K. Rakyan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - John Attwood
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Matthias Burger
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - John Burton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Tony V. Cox
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Rob Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas A. Down
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | | | - Roger Horton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Kevin Howe
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - David K. Jackson
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | | | - Christoph Koenig
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Jennifer Liddle
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - David Niblett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas Otto
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Roger Pettett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Stefanie Seemann
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | | | - Tony West
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Jane Rogers
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Alex Olek
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Kurt Berlin
- Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
| | - Stephan Beck
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
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Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton MR, Wooster R. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer 2004; 91:355-8. [PMID: 15188009 PMCID: PMC2409828 DOI: 10.1038/sj.bjc.6601894] [Citation(s) in RCA: 931] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The discovery of mutations in cancer genes has advanced our understanding of cancer. These results are dispersed across the scientific literature and with the availability of the human genome sequence will continue to accrue. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website have been developed to store somatic mutation data in a single location and display the data and other information related to human cancer. To populate this resource, data has currently been extracted from reports in the scientific literature for somatic mutations in four genes, BRAF, HRAS, KRAS2 and NRAS. At present, the database holds information on 66 634 samples and reports a total of 10 647 mutations. Through the web pages, these data can be queried, displayed as figures or tables and exported in a number of formats. COSMIC is an ongoing project that will continue to curate somatic mutation data and release it through the website.
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Affiliation(s)
- S Bamford
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - E Dawson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S Forbes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J Clements
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R Pettett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A Dogan
- Department of Histopathology, Royal Free and University Medical School, University Street, London WC1E 6JJ, UK
| | - A Flanagan
- The Institute of Orthopaedics, UCL, Stanmore, Middlesex HA7 4LP, UK
| | - J Teague
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - P A Futreal
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. E-mail:
| | - M R Stratton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R Wooster
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, Clamp M. An overview of Ensembl. Genome Res 2004; 14:925-8. [PMID: 15078858 PMCID: PMC479121 DOI: 10.1101/gr.1860604] [Citation(s) in RCA: 305] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of individual genomes, and of the synteny and orthology relationships between them. It is also a framework for integration of any biological data that can be mapped onto features derived from the genomic sequence. Ensembl is available as an interactive Web site, a set of flat files, and as a complete, portable open source software system for handling genomes. All data are provided without restriction, and code is freely available. Ensembl's aims are to continue to "widen" this biological integration to include other model organisms relevant to understanding human biology as they become available; to "deepen" this integration to provide an ever more seamless linkage between equivalent components in different species; and to provide further classification of functional elements in the genome that have been previously elusive.
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Affiliation(s)
- Ewan Birney
- EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, Curwen V, Cutts T, Down T, Durbin R, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz H, Iyer V, Kahari A, Jekosch K, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark C, Clamp M, Hubbard T. Ensembl 2004. Nucleic Acids Res 2004; 32:D468-70. [PMID: 14681459 PMCID: PMC308772 DOI: 10.1093/nar/gkh038] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.2] [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: 11/13/2022] Open
Abstract
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.
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Affiliation(s)
- E Birney
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H, Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Birney E. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res 2003; 31:38-42. [PMID: 12519943 PMCID: PMC165530 DOI: 10.1093/nar/gkg083] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.
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Affiliation(s)
- M Clamp
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M. The Ensembl genome database project. Nucleic Acids Res 2002; 30:38-41. [PMID: 11752248 PMCID: PMC99161 DOI: 10.1093/nar/30.1.38] [Citation(s) in RCA: 1062] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.
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Affiliation(s)
- T Hubbard
- The Wellcome Trust Sanger Institute and European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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