The vertebrate genome annotation (Vega) database

Nucleic Acids Research

Volumn 36, Issue SUPPL. 1, 2008, Pages

  Wilming, L G ^a   Gilbert, J G R ^a   Howe, K ^a   Trevanion, S ^a   Hubbard, T ^a   Harrow, J L ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; COMPUTER INTERFACE; DOG; GENE LOCUS; GENE SEQUENCE; GENOME ANALYSIS; HAPLOTYPE; HUMAN CHROMOSOME; INTERNET; ONLINE SYSTEM; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SWINE; VERTEBRATE GENOME ANNOTATION; ZEBRA FISH;

ALTERNATIVE SPLICING; ANIMALS; DATABASES, NUCLEIC ACID; GENOME, HUMAN; GENOMICS; HUMANS; INTERNET; MAJOR HISTOCOMPATIBILITY COMPLEX; MICE; MICE, INBRED NOD; MICE, KNOCKOUT; USER-COMPUTER INTERFACE; ZEBRAFISH;

CANIS FAMILIARIS; DANIO RERIO; SUIDAE; VERTEBRATA;

EID: 38549148703     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm987     Document Type: Article

References (25)

1. Sprague,J., Bayraktaroglu,L., Clements,D., Conlin,T., Fashena,D., Frazer,K., Haendel,M., Howe,D.G., Mani,P. et al. (2006) The Zebrafish Information Network: The zebrafish model organism database. Nucleic Acids Res., 34, D581-D585.
2. Ashurst,J.L., Chea,C.K., Gilbert,J.G., Jekosch,K., Keenan, S., Meidl,P., Searle,S.M., Stalker,J., Storey,R. et al. (2005) The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res., 33, D459-D465.
3. ENCODE Project Consortium. (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306, 636-640.
4. Birney,E., Stamatoyannopoulos,J.A., Dutta, A., Guigo,R., Gingeras,T.R., Margulies,E.H., Weng, Z., Snyder, M., Dermitzakis, E.T. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816.
5. Guigo,R., Flicek,P., Abril,J.F., Reymond,A., Lagarde,J., Denoeud,F., Antonarakis,S., Ashburner,M., Bajic,V.B. et al. (2006) EGASP: The human ENCODE Genome Annotation Assessment Project. Genome. Biol., 7 (Suppl 1), S2. 1-31.
6. Harrow,J., Denoeud, F., Frankish,A., Reymond,A., Chen,C.K., Chrast,J., Lagarde,J., Calbert,J.G., Storey,R. et al. (2006) GENCODE: producing a reference annotation for ENCODE. Genome. Biol., 7 (Suppl 1), S4. 1-9.
7. Tress,M.L., Martelli,P.L., Frankish,A., Reeves,G.A., Wesselink,J.J., Yeats,C., Olason,P.L., Albrecht,M., Hegyi,H., et al. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc. Natl Acad. Sci. USA 104, 5495-5500.
8. Hart,E.A., Caccamo,M., Harrow,J.L., Humphray,S.J, Gilbert,J.G., Trevanion,S., Hubbard,T., Rogers,J. and Rothschild,M.F. (2007) Lessons learned from the initial sequencing of the pig genome: Comparative analysis of an 8 Mb region of pig chromosome 17. Genome. Biol., 8, R168.
9. Renard,C., Hart, E., Sehra,H., Beasley,H.; Coggill,P., Howe,K., Harrow,J., Gilbert,J., Sims,S. et al. (2006)The genomic sequence and analysis of the swine major histocompatibility complex. Genomics 88, 96-110.
10. Horton, R., Coggill,P., Miretti,M.M., Sambrook,J.G., Traherne,J.A., Ward,R., Sims,S., Palmer,S., Sehra,H. et al. (2006) The LaRC haplotype, project: A-resource for killer immunoglobulin-like receptor-linked association studies. Tissue Antigens, 68, 450-452.
11. Sambrook,J.G., Sehra,H., Coggill,P., Humphray,S., Palmer,S., Sims,S., Takamatsu,H.H., Wileman, T., Archicald,A.L. et al. (2006) Identification of a single killer immunoglobulin-like receptor (KFR) gene in the porcine leukocyte receptor-complex on chromosome 6q. Immunogenetics, 58, 481-486.
12. Eaves,I.A., Wicker,L.S., Ghandour,G., Lyons,P.A., Peterson,L.B., Todd,J.A. and Glynne,R.J. (2002) Combining mouse congenic strains and microarray gene expression analyses to study a complex trait: The NOD model of type 1 diabetes. Genome Res., 12, 232-243.
13. Prochazka,M., Leiter,E.H., Serreze,D.V. and Coleman,D.L. (1987) Three recessive loci required, for insulin-dependent diabetes in nonobese diabetic mice. Science, 237, 286-289.
14. Wicker,L.S., Todd,J.A. and Peterson,L.B. (1995) Genetic control of autoimmune diabetes in the NOD mouse. Annu. Rev. Immunol.; 13 179-200.
15. Allcock,R.J., Atrazhev,A.M., Beck,S., de Jong,P.J., Elliott,J.F., Forbes,S., Halls,K., Horton,R., Osoegawa, K. et al. (2002) The MHC haplotype project: A resource for HLA-linked association studies. Tissue Antigens, 59, 520-521.
16. Stewart,C.A., Horton,R., Allcock,R.J., Ashurst,J.L., Atrazhev,A.M., Coggill,P., Dunham,I., Forbes,S., Halls,K. et al. (2004) Complete MHC haplotype sequencing for common disease gene mapping. Genome Res. 14, 1176-1187.
17. Traheme,J.A., Horton,R., Roberts,A.N., Miretti,M.M., Hurles,M.E., Stewart,C.A., Ashurst,J.L., Atrazhev,A.M., Coggill,P. et al. (2006) Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. PLoS Genet., 2, e9.
18. Debenham,S.L., Hart,E.A., Ashurat,J.L., Howe,K.L., Quail,M.A., Ollier,W.E. and Binns,M.M. (2005) Genomic sequence of the class II region of the canine MHC: Comparison with the MHC of other mammalian species. Genomics, 85, 48-59.
19. The BioSapiens Network of Excellence. (2005) Research networks: BioSapiens: A European network for integrated genome annotation. Eur. J. Hum. Genet., 13, 994-997.
20. Han,A., Kim,W.Y. and Park,S.M. (2007) SNP2NMD: A database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay. Bioinformatics, 23, 397-399.
21. Birney,E., Andrews,T.D., Bevan,P., Caccamo,M., Chon,Y., Clarke,L., Coates,G., Cuff,J., Curwen,V. et al. (2004) An overview of Ensembl. Genome Res., 14, 925-928.
22. Hubbard,T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
23. Hubbard,T.J., Aken,B.L., Beal,K., Ballester,B., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cunningham, F. et al. (2007) Ensembl 2007. Nucleic Acids Res., 35, D610-D617.
24. Gilbert,D. (2003) Shopping in the genome market with EnsMart. Brief Bioinform., 4, 292-296.
25. Kasprzyk,A., Keefe,D., Smedley,D., London,D., Spooner,W., Melsopp,C., Hammond,M., Rocca-Serra,P., Cox,T. et al. (2004) EnsMart: A generic system for fast and flexible access to biological data. Genome Res., 14, 160-169.