ENCODE whole-genome data in the UCSC Genome Browser: Update 2012

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Rosenbloom, Kate R ^a   Dreszer, Timothy R ^a   Long, Jeffrey C ^a   Malladi, Venkat S ^a   Sloan, Cricket A ^a   Raney, Brian J ^a   Cline, Melissa S ^a   Karolchik, Donna ^a   Barber, Galt P ^a   Clawson, Hiram ^a   Diekhans, Mark ^a   Fujita, Pauline A ^a   Goldman, Mary ^a   Gravell, Robert C ^a   Harte, Rachel A ^a   Hinrichs, Angie S ^a   Kirkup, Vanessa M ^a   Kuhn, Robert M ^a   Learned, Katrina ^a   Maddren, Morgan ^a   Meyer, Laurence R ^a   Pohl, Andy ^a,b   Rhead, Brooke ^a   Wong, Matthew C ^a   Zweig, Ann S ^a   Haussler, David ^a,c   Kent, W James ^a   more..

^a University of California Santa Cruz   (United States)

^b CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ANIMAL CELL; ANIMAL GENETICS; ANIMAL TISSUE; ARTICLE; BIOASSAY; BIOCHEMICAL ASSAY; CLIENT SERVER APPLICATION; ENCYCLOPEDIA OF DNA ELEMENTS CONSORTIUM WHOLE GENOME DATA; GENETIC DATABASE; GENOMICS; HUMAN; HUMAN CELL; HUMAN GENOME; HUMAN TISSUE; INFORMATION PROCESSING; MOUSE; NONHUMAN; PRIORITY JOURNAL; UNITED STATES; WEB BROWSER;

ANIMALS; DATABASES, NUCLEIC ACID; GENOME; GENOME, HUMAN; HUMANS; INTERNET; MICE; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE;

EID: 84861859517     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1012     Document Type: Article

References (21)

1. ENCODE Consortium. (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306, 636-640.
2. The ENCODE Project Consortium, Birney,E., Stamatoyannopoulos,J., Dutta,A., Guigó, R., Gingeras,T., Margulies,E., Weng,Z., Snyder,M., Dermitzakis,E. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816.
3. Myers,R.M., Stamatoyannopoulos,J., Snyder,M., Dunham,I., Hardison,R.C., Bernstein,B.E., Gingeras,T.R., Kent,W.J., Birney,E., Wold,B. et al. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046.
4. Rosenbloom,K.R., Dreszer,T.R., Pheasant,M., Barber,G.P., Meyer,L.R., Pohl,A., Raney,B.J., Wang,T., Hinrichs,A.S., Zweig,A.S. et al. (2010) ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res., 38, D620-D625.
5. Raney,B.J., Cline,M.S., Rosenbloom,K.R., Dreszer,T.R., Learned,K., Barber,G.P., Meyer,L.R., Sloan,C.A., Malladi,V.S., Roskin,K.M. et al. (2011) ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res., 39, D871-D875.
6. Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006. (Pubitemid 34662293)
7. Fujita,P.A., Rhead,B., Zweig,A.S., Hinrichs,A.S., Karolchik,D., Cline,M.S., Goldman,M., Barber,G.P., Clawson,H., Coelho,A. et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res., 39, D876-D882.
8. Li,H., Handsaker,B., Wysoker,A., Fennell,T., Ruan,J., Homer,N., Marth,G., Abecasis,G. and Durbin,R. (2009). 1000 Genome Project Data Processing Subgroup. (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-2079.
9. Kent,W.J., Zweig,A.S., Barber,G., Hinrichs,A.S. and Karolchik,D. (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics, 26, 2204-2207.
10. Dostie,J., Richmond,T.A., Arnaout,R.A., Selzer,R.R., Lee,W.L., Honan,T.A., Rubio,E.D., Krumm,A., Lamb,J., Nusbaum,C. et al. (2006) Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res., 16, 1299-1309. (Pubitemid 44506963)
11. Li,G., Fullwood,M.J., Xu,H., Mulawadi,F.H., Velkov,S., Vega,V., Ariyaratne,P.N., Mohamed,Y.B., Ooi,H.S., Tennakoon,C. et al. (2010) ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol., 11, R22.
12. Harrow,J., Denoeud,F., Frankish,A., Reymond,A., Chen,C.K., Chrast,J., Lagarde,J., Gilbert,J.G., Storey,R., Swarbreck,D. et al. (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol., 7(Suppl. 1), S41-S49.
13. The UniProt Consortium. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
14. Pruitt,K.D., Tatusova,T., Klimke,W. and Maglott,D.R. (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res., 37, D32-D36.
15. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2007) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65. (Pubitemid 46056171)
16. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Sayers,E.W. (2011) GenBank. Nucleic Acids Res., 39, D32-D37.
17. Krug,K., Nahnsen,S. and Macek,B. (2011) Mass spectrometry at the interface of proteomics and genomics. Mol Biosyst., 7, 284-291.
18. Poser,I., Sarov,M., Hutchins,J.R., Heriche,J.K., Toyoda,Y., Pozniakovsky,A., Weigl,D., Nitzsche,A., Hegemann,B., Bird,A.W. et al. (2008) BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods., 5, 409-415. (Pubitemid 351619099)
19. Ernst,J., Kheradpour,P., Mikkelsen,T.S., Shoresh,N., Ward,L.D., Epstein,C.B., Zhang,X., Wang,L., Issner,R., Coyne,M. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49.
20. Bernstein,B.E., Stamatoyannopoulos,J.A., Costello,J.F., Ren,B., Milosavljevic,A., Meissner,A., Kellis,M., Marra,M.A., Beaudet,A.L., Ecker,J.R. et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol., 28, 1045-1048.
21. Barrett,T., Troup,D.B., Wilhite,S.E., Ledoux,P., Rudnev,D., Evangelista,C., Kim,I.F., Soboleva,A., Tomashevsky,M. and Edgar,R. (2007) NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res., 35, D760-D765. (Pubitemid 46056306)