The UCSC Genome Browser database: 2021 update

被引：313

作者：

Gonzalez, Jairo Navarro ^{[1
]}

Zweig, Ann S. ^{[1
]}

Speir, Matthew L. ^{[1
]}

Schmelter, Daniel ^{[1
]}

Rosenbloom, Kate R. ^{[1
]}

Raney, Brian J. ^{[1
]}

Powell, Conner C. ^{[1
]}

Nassar, Luis R. ^{[1
]}

Maulding, Nathan D. ^{[1
]}

Lee, Christopher M. ^{[1
]}

Lee, Brian T. ^{[1
]}

Hinrichs, Angie S. ^{[1
]}

Fyfe, Alastair C. ^{[1
]}

Fernandes, Jason D. ^{[1
]}

Diekhans, Mark ^{[1
]}

Clawson, Hiram ^{[1
]}

Casper, Jonathan ^{[1
]}

Benet-Pages, Anna ^{[1
,2
]}

Barber, Galt P. ^{[1
]}

Haussler, David ^{[1
,3
]}

Kuhn, Robert M. ^{[1
]}

Haeussler, Maximilian ^{[1
]}

Kent, W. James ^{[1
]}

机构：

[1] Univ Calif Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA

[2] Med Genet Ctr MGZ, Munich, Germany

[3] Univ Calif Santa Cruz, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA

来源：

NUCLEIC ACIDS RESEARCH | 2021年 / 49卷 / D1期

基金：

美国国家卫生研究院;

关键词：

READ ALIGNMENT; REFERENCE SEQUENCE; PROVIDES; SYSTEM;

D O I：

10.1093/nar/gkaa1070

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.

引用

页码：D1046 / D1057

页数：12

共 46 条

[1] The GTEx Consortium atlas of genetic regulatory effects across human tissues [J].

Aguet, Francois ;

Barbeira, Alvaro N. ;

Bonazzola, Rodrigo ;

Brown, Andrew ;

Castel, Stephane E. ;

Jo, Brian ;

Kasela, Silva ;

Kim-Hellmuth, Sarah ;

Liang, Yanyu ;

Parsana, Princy ;

Flynn, Elise ;

Fresard, Laure ;

Gamazon, Eric R. ;

Hamel, Andrew R. ;

He, Yuan ;

Hormozdiari, Farhad ;

Mohammadi, Pejman ;

Munoz-Aguirre, Manuel ;

Ardlie, Kristin G. ;

Battle, Alexis ;

Bonazzola, Rodrigo ;

Brown, Christopher D. ;

Cox, Nancy ;

Dermitzakis, Emmanouil T. ;

Engelhardt, Barbara E. ;

Garrido-Martin, Diego ;

Gay, Nicole R. ;

Getz, Gad ;

Guigo, Roderic ;

Hamel, Andrew R. ;

Handsaker, Robert E. ;

He, Yuan ;

Hoffman, Paul J. ;

Hormozdiari, Farhad ;

Im, Hae Kyung ;

Jo, Brian ;

Kasela, Silva ;

Kashin, Seva ;

Kim-Hellmuth, Sarah ;

Kwong, Alan ;

Lappalainen, Tuuli ;

Li, Xiao ;

Liang, Yanyu ;

MacArthur, Daniel G. ;

Mohammadi, Pejman ;

Montgomery, Stephen B. ;

Munoz-Aguirre, Manuel ;

Rouhana, John M. ;

Hormozdiari, Farhad ;

Im, Hae Kyung .

SCIENCE, 2020, 369 (6509) :1318-1330

[2] An atlas of active enhancers across human cell types and tissues [J].

Andersson, Robin ;

Gebhard, Claudia ;

Miguel-Escalada, Irene ;

Hoof, Ilka ;

Bornholdt, Jette ;

Boyd, Mette ;

Chen, Yun ;

Zhao, Xiaobei ;

Schmidl, Christian ;

Suzuki, Takahiro ;

Ntini, Evgenia ;

Arner, Erik ;

Valen, Eivind ;

Li, Kang ;

Schwarzfischer, Lucia ;

Glatz, Dagmar ;

Raithel, Johanna ;

Lilje, Berit ;

Rapin, Nicolas ;

Bagger, Frederik Otzen ;

Jorgensen, Mette ;

Andersen, Peter Refsing ;

Bertin, Nicolas ;

Rackham, Owen ;

Burroughs, A. Maxwell ;

Baillie, J. Kenneth ;

Ishizu, Yuri ;

Shimizu, Yuri ;

Furuhata, Erina ;

Maeda, Shiori ;

Negishi, Yutaka ;

Mungall, Christopher J. ;

Meehan, Terrence F. ;

Lassmann, Timo ;

Itoh, Masayoshi ;

Kawaji, Hideya ;

Kondo, Naoto ;

Kawai, Jun ;

Lennartsson, Andreas ;

Daub, Carsten O. ;

Heutink, Peter ;

Hume, David A. ;

Jensen, Torben Heick ;

Suzuki, Harukazu ;

Hayashizaki, Yoshihide ;

Mueller, Ferenc ;

Forrest, Alistair R. R. ;

Carninci, Piero ;

Rehli, Michael ;

Sandelin, Albin .

NATURE, 2014, 507 (7493) :455-+

[3] Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA [J].

Andrews, RM ;

Kubacka, I ;

Chinnery, PF ;

Lightowlers, RN ;

Turnbull, DM ;

Howell, N .

NATURE GENETICS, 1999, 23 (02) :147-147

[4] High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression [J].

Batut, Philippe ;

Dobin, Alexander ;

Plessy, Charles ;

Carninci, Piero ;

Gingeras, Thomas R. .

GENOME RESEARCH, 2013, 23 (01) :169-180

[5]

Benson DA, 2007, NUCLEIC ACIDS RES, V35, pD21, DOI [10.1093/nar/gkw1070, 10.1093/nar/gkl986, 10.1093/nar/gkp1024, 10.1093/nar/gkx1094, 10.1093/nar/gks1195, 10.1093/nar/gkn723, 10.1093/nar/gkg057, 10.1093/nar/gkq1079, 10.1093/nar/gkr1202]

[6] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[7] AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature [J].

Birgmeier, Johannes ;

Deisseroth, Cole A. ;

Hayward, Laura E. ;

Galhardo, Luisa M. T. ;

Tierno, Andrew P. ;

Jagadeesh, Karthik A. ;

Stenson, Peter D. ;

Cooper, David N. ;

Bernstein, Jonathan A. ;

Haeussler, Maximilian ;

Bejerano, Gill .

GENETICS IN MEDICINE, 2020, 22 (02) :362-370

[8] Genenames.org: the HGNC and VGNC resources in 2019 [J].

Braschi, Bryony ;

Denny, Paul ;

Gray, Kristian ;

Jones, Tamsin ;

Seal, Ruth ;

Tweedie, Susan ;

Yates, Bethan ;

Bruford, Elspeth .

NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D786-D792

[9] Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines [J].

Bui, Huynh-Hoa ;

Sidney, John ;

Li, Wei ;

Fusseder, Nicolas ;

Sette, Alessandro .

BMC BIOINFORMATICS, 2007, 8 (1)

[10] The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic [J].

The COVID-19 Host Genetics Initiative .

EUROPEAN JOURNAL OF HUMAN GENETICS, 2020, 28 (06) :715-718

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