GENCODE

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GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project.

The aim of the GENCODE project is to annotate all evidence-based gene features in the entire human genome at a high accuracy.[1][2] The result will be a set of annotations including all protein-coding loci with alternatively transcribed variants,[3] non-coding loci [4] with transcript evidence, and pseudogenes.[5] Annotation of the GENCODE gene set is carried out using a mix of manual annnotation, experimental analysis and computational biology methods. Since September 2009 GENCODE has been the human gene set used by the Ensembl project and each new GENCODE release corresponds to an Ensembl release.

The GENCODE project is an international effort headed by Tim Hubbard at the Wellcome Trust Sanger Institute.

See also

References

  1. Harrow J, Denoeud F, Frankish A, et al. (2006). "GENCODE: producing a reference annotation for ENCODE". Genome Biol. 7 (Suppl 1): S4.1–9. doi:10.1186/gb-2006-7-s1-s4. PMC 1810553. PMID 16925838. 
  2. Harrow, J; Frankish, A; Gonzalez, JM; Tapanari, E; Diekhans, M; Kokocinski, F; Aken, BL; Barrell, D; Zadissa, A; Searle, S; Barnes, I; Bignell, A; Boychenko, V; Hunt, T; Kay, M; Mukherjee, G; Rajan, J; Despacio-Reyes, G; Saunders, G; Steward, C; Harte, R; Lin, M; Howald, C; Tanzer, A; Derrien, T; Chrast, J; Walters, N; Balasubramanian, S; Pei, B; Tress, M; Rodriguez, JM; Ezkurdia, I; van Baren, J; Brent, M; Haussler, D; Kellis, M; Valencia, A; Reymond, A; Gerstein, M; Guigó, R; Hubbard, TJ (2012 Sep). "GENCODE: the reference human genome annotation for The ENCODE Project.". Genome Research 22 (9): 1760–74. doi:10.1101/gr.135350.111. PMC 3431492. PMID 22955987. 
  3. Frankish, A; Mudge, JM; Thomas, M; Harrow, J (2012). "The importance of identifying alternative splicing in vertebrate genome annotation.". Database : the journal of biological databases and curation 2012: bas014. doi:10.1093/database/bas014. PMC 3308168. PMID 22434846. 
  4. Derrien, T; Johnson, R; Bussotti, G; Tanzer, A; Djebali, S; Tilgner, H; Guernec, G; Martin, D; Merkel, A; Knowles, DG; Lagarde, J; Veeravalli, L; Ruan, X; Ruan, Y; Lassmann, T; Carninci, P; Brown, JB; Lipovich, L; Gonzalez, JM; Thomas, M; Davis, CA; Shiekhattar, R; Gingeras, TR; Hubbard, TJ; Notredame, C; Harrow, J; Guigó, R (2012 Sep). "The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.". Genome Research 22 (9): 1775–89. doi:10.1101/gr.132159.111. PMC 3431493. PMID 22955988. 
  5. Pei, B; Sisu, C; Frankish, A; Howald, C; Habegger, L; Mu, XJ; Harte, R; Balasubramanian, S; Tanzer, A; Diekhans, M; Reymond, A; Hubbard, TJ; Harrow, J; Gerstein, MB (2012 Sep 5). "The GENCODE pseudogene resource.". Genome Biology 13 (9): R51. doi:10.1186/gb-2012-13-9-r51. PMC 3491395. PMID 22951037. 

External links

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