The UCSC Genome Browser database: 2022 update
Open accessAbstract
The UCSC Genome Browser, https://genome.ucsc.edu, is a graphical viewer for exploring genome annotations. The website provides integrated tools for visualizing, comparing, analyzing, and sharing both publicly available and user-generated genomic datasets. Data highlights this year include a collection of easily accessible public hub assemblies on new organisms, now featuring BLAT alignment and PCR capabilities, and new and updated clinical tracks (gnomAD, DECIPHER, CADD, REVEL). We introduced a new Track Sets feature and enhanced variant displays to aid in the interpretation of clinical data. We also added a tool to rapidly place new SARS-CoV-2 genomes in a global phylogenetic tree enabling researchers to view the context of emerging mutations in our SARS-CoV-2 Genome Browser. Other new software focuses on usability features, including more informative mouseover displays and new fonts.
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A majority of novel TSSs were supported by spliced transcripts from RNA-seq and expressed sequence tags.
“A majority of the novel TSSs were supported by spliced transcripts (see methods) from RNA-seq25,26 and expressed sequence tag27”
From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [27]
The NEW GENOME BROWSER DATA section describes genome-browser tracks, but does not report whether novel TSSs were supported by spliced transcripts. Searches for “expressed sequence tag,” “EST,” and “transcription start sites” found no passage establishing that the cited browser update supplied the EST evidence or the claimed majority. (LLM, conf=0.72)
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Cites
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works
Self-citationClinVar: improving access to variant interpretations and supporting evidence
Landrum, M. J., Lee, J. M., Benson, M., Brown, G. R., Chao, C., Chitipiralla, S., Gu, B., Hart, J., Hoffman, D., Jang, W., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1153 · Cited by 4,196 · cited 3× · see citing works
“As an example, our ClinVar SNVs and ClinGen tracks now include a more detailed mouseover display to facilitate the faster assessment of phenotype and clinical significance.”
InfluentialExtensive sequencing of seven human genomes to characterize benchmark reference materials
Zook, J. M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., Weng, Z., Liu, Y., Mason, C. E., Alexander, N., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.25 · Cited by 811 · cited 1× · see citing works
“Tovisualize phased personal genomics data, this year we released two new track sets featuring family trios from the Genome in a Bottle Consortium (7) and 1000 Genomes Project (8).”
UCSC Genome Browser enters 20th year
Lee, C. M., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., Gonzalez, J. N., Hinrichs, A. S., Lee, B. T., Nassar, L. R., Powell, C. C., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1012 · Cited by 191 · see citing works
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- Authors
- Lee, B. T., Barber, G. P., Benet-Pagès, A., Casper, J., Clawson, H., Diekhans, M., Fischer, C., Gonzalez, J. N., Hinrichs, A. S., Lee, C. M., Muthuraman, P., Nassar, L. R., Nguy, B., Pereira, T., Perez, G., Raney, B. J., Rosenbloom, K. R., Schmelter, D., Speir, M. L., Wick, B. D., Zweig, A. S., Haussler, D., Kuhn, R. M., Haeussler, M., & Kent, W. J.
- Affiliations
- University of California, Santa Cruz (US)
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Corresponding author
- Lee, Brian T
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-10-28
- Volume
- 50
- Issue
- D1
- Pages
- D1115-D1122
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC8728131
- OpenAlex
- W3208459100
- Cited by
- 273
- References
- 4
- Citations by year
- 2026: 17 · 2025: 37 · 2024: 68 · 2023: 86 · 2022: 62 · 2021: 2
- FWCI
- 18.99
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- National Human Genome Research Institute (5U41HG002371, 5U41HG007234, 5R01HG010329)
- National Institutes of Health (5U01HG010971)
- U.S. Department of Health and Human Services (1U41HG010972)
- Howard Hughes Medical Institute (090100)
- Silicon Valley Community Foundation (2017-171531(5022))
- Center for Information Technology Research in the Interest of Society (2020-0000000026)
- University of California Office of the President Emergency (R00RG2456)
- California Department of Public Health (20-11088)
- California HIV/AIDS Research Program (R01RG3764)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- UCSC Genome Browser, genome browser, PCR, gnomAD, DECIPHER, CADD, REVEL, variant interpretation, SARS-CoV-2 genome, phylogenetic tree
- MeSH terms
- Exome Sequencing, SARS-CoV-2, Animals, Humans, Phylogeny, User-Computer Interface, Genome, Human, Polymerase Chain Reaction, Databases, Genetic, Web Browser
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