GENCODE: producing a reference annotation for ENCODE

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Harrow J, Denoeud F, Frankish A, Reymond A, Chen C, Chrast J, Lagarde J, Gilbert J G, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis S E, Guigo R. GENCODE: producing a reference annotation for ENCODE. Genome Biology. 2006; 7 Supl 1: S4. DOI 10.1186/gb-2006-7-s1-s4
http://hdl.handle.net/10230/12925
To cite or link this document: http://hdl.handle.net/10230/12925
dc.contributor.author Harrow, Jennifer
dc.contributor.author Denoeud, France
dc.contributor.author Frankish, Adam
dc.contributor.author Reymond, Alexandre
dc.contributor.author Chen, Chao-Kung
dc.contributor.author Chrast, Jacqueline
dc.contributor.author Lagarde, Julien
dc.contributor.author Gilbert, James GR
dc.contributor.author Storey, Roy
dc.contributor.author Swarbreck, David
dc.contributor.author Rossier, Colette
dc.contributor.author Ucla, Catherine
dc.contributor.author Hubbard, Tim J.
dc.contributor.author Antonarakis, Stylianos E.
dc.contributor.author Guigó Serra, Roderic
dc.contributor.other Universitat Pompeu Fabra
dc.date.accessioned 2011-10-26T11:07:50Z
dc.date.available 2011-10-26T11:07:50Z
dc.date.issued 2006
dc.identifier.citation Harrow J, Denoeud F, Frankish A, Reymond A, Chen C, Chrast J, Lagarde J, Gilbert J G, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis S E, Guigo R. GENCODE: producing a reference annotation for ENCODE. Genome Biology. 2006; 7 Supl 1: S4. DOI 10.1186/gb-2006-7-s1-s4
dc.identifier.issn 1465-6906
dc.identifier.uri http://hdl.handle.net/10230/12925
dc.description.abstract Background: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. Results: The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5’ rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5’ extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. Conclusions: In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5’ RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.
dc.language.iso eng
dc.publisher BioMed Central
dc.rights © 2006 Harrow et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is also available at http://genomebiology.com/2006/7/S1/S4
dc.rights.uri http://creativecommons.org/licenses/by/2.0
dc.subject.other Bioinformàtica
dc.subject.other Biologia molecular -- Tècnica
dc.title GENCODE: producing a reference annotation for ENCODE
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/gb-2006-7-s1-s4
dc.subject.keyword GENCODE
dc.subject.keyword ENCODE
dc.subject.keyword cDNA
dc.subject.keyword RACE
dc.subject.keyword Gene Loci
dc.type.version info:eu-repo/semantics/publishedVersion


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