ASTD: The Alternative Splicing and Transcript Diversity database

Gautier Koscielny; Vincent Le Texier; Chellappa Gopalakrishnan; Vasudev Kumanduri; Jean-Jack Riethoven; Francesco Nardone; Eleanor Stanley; Christine Fallsehr; Oliver Hofmann; Meelis Kull; Eoghan Harrington; Stéphanie Boué; Eduardo Eyras; Mireya Plass; Fabrice Lopez; William Ritchie; Virginie Moucadel; Takeshi Ara; Heike Pospisil; Alexander Herrmann; Jens G. Reich; Roderic Guigó; Peer Bork; Magnus von Knebel Doeberitz; Jaak Vilo; Winston Hide; Rolf Apweiler; Thangavel Alphonse Thanaraj; Daniel Gautheret

doi:10.1016/j.ygeno.2008.11.003

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ASTD: The Alternative Splicing and Transcript Diversity database

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ASTD: The Alternative Splicing and Transcript Diversity database

Gautier Koscielny, Vincent Le Texier, Chellappa Gopalakrishnan, Vasudev Kumanduri, Jean-Jack Riethoven, Francesco Nardone, Eleanor Stanley, Christine Fallsehr, Oliver Hofmann, Meelis Kull, …

Genomics (San Diego, Calif.), Vol.93(3), pp.213-220

01/03/2009

DOI: https://doi.org/10.1016/j.ygeno.2008.11.003

PMID: 19059335

Résumé

Alternative initiation

Alternative polyadenylation

Alternative splicing

Alternative transcription

The Alternative Splicing and Transcript Diversity database (ASTD) gives access to a vast collection of alternative transcripts that integrate transcription initiation, polyadenylation and splicing variant data. Alternative transcripts are derived from the mapping of transcribed sequences to the complete human, mouse and rat genomes using an extension of the computational pipeline developed for the ASD (Alternative Splicing Database) and ATD (Alternative Transcript Diversity) databases, which are now superseded by ASTD. For the human genome, ASTD identifies splicing variants, transcription initiation variants and polyadenylation variants in 68%, 68% and 62% of the gene set, respectively, consistent with current estimates for transcription variation. Users can access ASTD through a variety of browsing and query tools, including expression state-based queries for the identification of tissue-specific isoforms. Participating laboratories have experimentally validated a subset of ASTD-predicted alternative splice forms and alternative polyadenylation forms that were not previously reported. The ASTD database can be accessed at http://www.ebi.ac.uk/astd.

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Titre: ASTD: The Alternative Splicing and Transcript Diversity database
Créateurs - sans rôle: Gautier Koscielny - European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Vincent Le Texier - European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Chellappa Gopalakrishnan - European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Vasudev Kumanduri - European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Jean-Jack Riethoven - European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Francesco Nardone - European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Eleanor Stanley - European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Christine Fallsehr - Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraβe 1, 69117 Heidelberg, Germany
Oliver Hofmann - South African National Bioinformatics Institute, University Western Cape, Private Bag X17, Bellville 7535, South Africa
Meelis Kull - Estonian Biocenter, Riia 23b, 51010 Tartu, Estonia
Eoghan Harrington - Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraβe 1, 69117 Heidelberg, Germany
Stéphanie Boué - Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraβe 1, 69117 Heidelberg, Germany
Eduardo Eyras - Grup de Recerca en Informatica Biomedica, Institut Municipal d'Investigacio Medica, Universistat Pompeu Fabra, Plaça de la Mercè, 10-12, 08002 Barcelona, Spain
Mireya Plass - Grup de Recerca en Informatica Biomedica, Institut Municipal d'Investigacio Medica, Universistat Pompeu Fabra, Plaça de la Mercè, 10-12, 08002 Barcelona, Spain
Fabrice Lopez - INSERM U928, Université de la Méditerranée, case 928 - 163, Avenue de Luminy, 13288 Marseille cedex 09, France
William Ritchie - INSERM U928, Université de la Méditerranée, case 928 - 163, Avenue de Luminy, 13288 Marseille cedex 09, France
Virginie Moucadel - INSERM U928, Université de la Méditerranée, case 928 - 163, Avenue de Luminy, 13288 Marseille cedex 09, France
Takeshi Ara - INSERM U928, Université de la Méditerranée, case 928 - 163, Avenue de Luminy, 13288 Marseille cedex 09, France
Heike Pospisil - Center for Bioinformatics, University of Hamburg, Bundesstr.43, 20146 Hamburg, Germany
Alexander Herrmann - Institute for Clinical Molecular Biology, Christian-Albrechts University Kiel, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
Jens G. Reich - Dept. of Bioinformatics, Max-Delbrueck-Center for Molecular Medicine Berlin-Buch, Robert-Roessle-Str. 10, 13125 Berlin, Germany
Roderic Guigó - Grup de Recerca en Informatica Biomedica, Institut Municipal d'Investigacio Medica, Universistat Pompeu Fabra, Plaça de la Mercè, 10-12, 08002 Barcelona, Spain
Peer Bork - Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraβe 1, 69117 Heidelberg, Germany
Magnus von Knebel Doeberitz - Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 220, D-69120 Heidelberg, Germany
Jaak Vilo - Estonian Biocenter, Riia 23b, 51010 Tartu, Estonia
Winston Hide - South African National Bioinformatics Institute, University Western Cape, Private Bag X17, Bellville 7535, South Africa
Rolf Apweiler - European Bioinformatics Institute
Thangavel Alphonse Thanaraj - European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Daniel Gautheret - INSERM U928, Université de la Méditerranée, case 928 - 163, Avenue de Luminy, 13288 Marseille cedex 09, France
Détails de publication: Genomics (San Diego, Calif.), Vol.93(3), pp.213-220
Éditeur: Elsevier Inc
Nombre de pages: 8
Identifiants: 99139665309311
Unité académique: Institut de Génétique Humaine - IGH
Langue: English
Type de ressource: Journal article