Ensembl 2016

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D710-D716

  Yates, Andrew ^a   Akanni, Wasiu ^a   Amode, M Ridwan ^a   Barrell, Daniel ^a,b   Billis, Konstantinos ^a   Carvalho Silva, Denise ^a   Cummins, Carla ^a   Clapham, Peter ^b   Fitzgerald, Stephen ^a   Gil, Laurent ^a   Girón, Carlos García ^a   Gordon, Leo ^a   Hourlier, Thibaut ^a   Hunt, Sarah E ^a   Janacek, Sophie H ^a   Johnson, Nathan ^a   Juettemann, Thomas ^a   Keenan, Stephen ^a   Lavidas, Ilias ^a   Martin, Fergal J ^a   Maurel, Thomas ^a   McLaren, William ^a   Murphy, Daniel N ^a   Nag, Rishi ^a   Nuhn, Michael ^a   Parker, Anne ^a   Patricio, Mateus ^a   Pignatelli, Miguel ^a   Rahtz, Matthew ^b   Riat, Harpreet Singh ^a   Sheppard, Daniel ^a   Taylor, Kieron ^a   Thormann, Anja ^a   Vullo, Alessandro ^a   Wilder, Steven P ^a   Zadissa, Amonida ^a   Birney, Ewan ^a   Harrow, Jennifer ^b   Muffato, Matthieu ^a   Perry, Emily ^a   Ruffier, Magali ^a   Spudich, Giulietta ^a   Trevanion, Stephen J ^a   Cunningham, Fiona ^a   Aken, Bronwen L ^a   Zerbino, Daniel R ^a   Flicek, Paul ^a,b   more..

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; GENOME; GENOME ANNOTATION; HUMAN GENOME; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INFORMATION SERVICE; INTERNET; MOBILE APPLICATION; PRIORITY JOURNAL; ANIMAL; GENE; GENETIC DATABASE; GENETIC VARIATION; GENETICS; GENOMICS; HUMAN; MOLECULAR GENETICS; MOUSE; RAT; REGULATORY SEQUENCE; SOFTWARE;

PROTEIN;

ANIMALS; DATABASES, GENETIC; GENES; GENETIC VARIATION; GENOMICS; HUMANS; INTERNET; MICE; MOLECULAR SEQUENCE ANNOTATION; PROTEINS; RATS; REGULATORY SEQUENCES, NUCLEIC ACID; SOFTWARE;

EID: 84976870685     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1157     Document Type: Article

References (49)

1. Rosenbloom, K.R., Armstrong, J., Barber, G.P., Casper, J., Clawson, H., Diekhans, M., Dreszer, T.R., Fujita, P.A., Guruvadoo, L., Haeussler, M. et al. (2015) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res., 43, D670-D681.
2. Pruitt, K.D., Brown, G.R., Hiatt, S.M., Thibaud-Nissen, F., Astashyn, A., Ermolaeva, O., Farrell, C.M., Hart, J., Landrum, M.J., McGarvey, K.M. et al. (2014) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res., 42, D756-D763.
3. ENCODE, Project Consortium. (2012) An integrated encyclopaedia of DNA elements in the human genome. Nature, 489, 57-74.
4. Church, D.M., Schneider, V.A., Graves, T., Auger, K., Cunningham, F., Bouk, N., Chen, H.-C., Agarwala, R., McLaren, W.M., Ritchie, G.R.S. et al. (2011) Modernizing reference genome assemblies. PLoS Biol., 9, e1001091.
5. Harrow, J., Frankish, A., Gonzalez, J.M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B.L., Barrell, D., Zadissa, A., Searle, S. et al. (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res., 22, 1760-1774.
6. UniProt Consortium. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.
7. Roadmap Epigenomics Consortium. (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518, 317-330.
8. Zerbino, D.R., Wilder, S.P., Johnson, N., Juettemann, T. and Flicek, P.R. (2015) The Ensembl Regulatory Build. Genome Biol., 16, 56.
9. Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M. and Sirotkin, K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
10. Stenson, P.D., Ball, E.V., Mort, M., Phillips, A.D., Shiel, J.A., Thomas, N.S.T., Abeysinghe, S., Krawczak, M. and Cooper, D.N. (2003) Human Gene Mutation Database (HGMD): 2003 update. Hum. Mutat., 21, 577-581.
11. Landrum, M.J., Lee, J.M., Riley, G.R., Jang, W., Rubinstein, W.S., Church, D.M. and Maglott, D.R. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res., 42, D980-D985.
12. Kersey, P.J., Allen, J.E., Christensen, M., Davis, P., Falin, L.J., Grabmueller, C., Hughes, D.S.T., Humphrey, J., Kerhornou, A., Khobova, J. et al. (2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res., 42, D546-D552.
13. McLaren, W., Pritchard, B., Rios, D., Chen, Y., Flicek, P. and Cunningham, F. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics, 26, 2069-2070.
14. Zhao, H., Sun, Z., Wang, J., Huang, H., Kocher, J.-P. and Wang, L. (2014) CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics, 30, 1006-1007.
15. 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.
16. Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R., Lunter, G., Marth, G., Sherry, S.T. et al. (2011) The Variant Call Format and VCFtools. Bioinformatics, 27, 2156-2158.
17. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
18. Raney, B.J., Dreszer, T.R., Barber, G.P., Clawson, H., Fujita, P.A., Wang, T., Nguyen, N., Paten, B., Zweig, A.S., Karolchik, D. et al. (2014) Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics, 30, 1003-1005.
19. Wilming, L.G., Gilbert, J.G.R., Howe, K., Trevanion, S., Hubbard, T. and Harrow, J.L. (2007) The vertebrate genome annotation (Vega) database. Nucleic Acids Res., 36, D753-D760.
20. Rodriguez, J.M., Carro, A., Valencia, A. and Tress, M.L. (2015) APPRIS WebServer and WebServices. Nucleic Acids Res., 43, W455-W459.
21. Frankish, A., Uszczynska, B., Ritchie, G.R., Gonzalez, J.M., Pervouchine, D., Petryszak, R., Mudge, J.M., Fonseca, N., Brazma, A., Guigo, R. et al. (2015) Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. BMC Genomics, 16, S2.
22. Pruitt, K.D., Harrow, J., Harte, R.A., Wallin, C., Diekhans, M., Maglott, D.R., Searle, S., Farrell, C.M., Loveland, J.E., Ruef, B.J. et al. (2009) The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res., 19, 1316-1323.
23. Amberger, J.S., Bocchini, C.A., Schiettecatte, F., Scott, A.F. and Hamosh, A. (2015) OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res., 43, D789-D798.
24. Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L. et al. (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res., 42, D1001-D1006.
25. Shimoyama, M., Pons, J., Hayman, G.T., Laulederkind, S.J.F., Liu, W., Nigam, R., Petri, V, Smith, J.R., Tutaj, M., Wang, S.-J. et al. (2015) The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. Nucleic Acids Res., 43, D743-D750.
26. Lenffer, J., Nicholas, F.W., Castle, K., Rao, A., Gregory, S., Poidinger, M., Mailman, M.D. and Ranganathan, S. (2006) OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI. Nucleic Acids Res., 34, D599-D601.
27. Hu, Z.-L., Park, C.A., Wu, X.-L. and Reecy, J.M. (2013) Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res., 41, D871-D879.
28. Sprague, J., Bayraktaroglu, L., Clements, D., Conlin, T, Fashena, D., Frazer, K., Haendel, M., Howe, D.G, Mani, P., Ramachandran, S. et al (2006) The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res., 34, D581-D585.
29. Ng, P.C. and Henikoff, S. (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res, 31, 3812-3814.
30. Ivan Adzhubei, D.M.J. (2013) Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2. Curr. Protoc. Hum. Genet., doi:10.1002/0471142905.hg0720s76.
31. Zhou, X., Lowdon, R.F, Li, D., Lawson, H.A., Madden, P.A.F, Costello, J.F and Wang, T (2013) Exploring long-range genome interactions using the WashU Epigenome Browser. Nat. Methods, 10, 375-376.
32. Paten, B., Herrero, J., Beal, K., Fitzgerald, S. and Birney, E. (2008) Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res., 18, 1814-1828.
33. Ruan, J., Li, H., Chen, Z., Coghlan, A., Coin, L.J.M., Guo, Y, Hériché, J.-K., Hu, Y, Kristiansen, K., Li, R. et al. (2008) TreeFam: 2008 Update. Nucleic Acids Res., 36, D735-D740.
34. Mi, H., Muruganujan, A. and Thomas, P.D. (2013) PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res., 41, D377-D386.
35. Sonnhammer, E.L.L., Gabaldón, T, Sousa da Silva, A.W., Martin, M., Robinson-Rechavi, M., Boeckmann, B., Thomas, P.D., Dessimoz, C and Quest for Orthologs consortium. (2014) Big data and other challenges in the quest for orthologs. Bioinformatics, 30, 2993-2998.
36. The 1000 Genomes Project Consortium. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.
37. Forbes, S.A., Beare, D., Gunasekaran, P., Leung, K., Bindal, N., Boutselakis, H., Ding, M., Bamford, S., Cole, C., Ward, S. et al. (2015) COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res., 43, D805-D811.
38. Exome Aggregation Consortium. (2015) Cambridge, http://exac.broadinstitute.org.
39. Tennessen, J.A., Bigham, A.W., O'Connor, T.D., Fu, W., Kenny, E.E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G. et al. (2012) Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science, 337, 64-69.
40. Liu, X., Jian, X. and Boerwinkle, E. (2013) dbNSFP v2.0: a Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations. Hum. Mutat., 34, E2393-E2402.
41. Petryszak, R., Burdett, T., Fiorelli, B., Fonseca, N.A., Gonzalez-Porta, M., Hastings, E., Huber, W., Jupp, S., Keays, M., Kryvych, N. et al. (2014) Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res., 42, D926-D932.
42. Illumina, Inc. (2015) Illumina Platinum Genomes. http://www.illumina.com/platinumgenomes/.
43. Mifsud, B., Tavares-Cadete, F., Young, A.N., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S.W., Andrews, S., Grey, W., Ewels, P.A. et al. (2015) Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat. Genet., 47, 598-606.
44. Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S. et al. (2015) Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol., 16, 22.
45. Lonsdale, J., Thomas, J., Salvatore, M., Phillips, R., Lo, E., Shad, S., Hasz, R., Walters, G., Garcia, F., Young, N. et al. (2013) The Genotype-Tissue Expression (GTEx) project. Nat. Genet., 45, 580-585.
46. Yates, A., Beal, K., Keenan, S., McLaren, W., Pignatelli, M., Ritchie, G.R.S., Ruffier, M., Taylor, K., Vullo, A. and Flicek, P. (2015) The Ensembl REST API: Ensembl Data for Any Language. Bioinformatics, 31, 143-145.
47. Severin, J., Beal, K., Vilella, A.J., Fitzgerald, S., Schuster, M., Gordon, L., Ureta-Vidal, A., Flicek, P. and Herrero, J. (2010) eHive: an artificial intelligence workflow system for genomic analysis. BMC Bioinformatics, 11, 240.
48. Kinsella, R.J., Kähäri, A., Haider, S., Zamora, J., Proctor, G., Spudich, G., Almeida-King, J., Staines, D., Derwent, P., Kerhornou, A. et al. (2011) Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford), 2011, bar030.
49. Durinck, S., Spellman, P.T., Birney, E., Bolstad, B., Dettling, M., Dudoit, S. and Huber, W. (2009) Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protoc., 4, 1184-1191.