The Human Genome Browser at UCSC
Open accessAbstract
As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu . This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.
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H3K9me2-based ChIP-sequencing was performed in biological duplicate and significantly H3K9me2 depleted genes were validated with quantitative PCR.
“To identify specific genes with reduced H3K9me2 levels, we performed H3K9me2-based ChIP-sequencing (ChIP-seq) in biological duplicate (Fig. 4a, http://genome.ucsc.edu30), and validated significantly H3K9me2 depleted genes with quantitative PCR (qPCR) (Fig. 4b).”
From Tau promotes neurodegeneration through global chromatin relaxation (2014) · cites this paper as [30]
The genomic region distal to the HSA2 fusion site maps well to the near-telomeric region of chimpanzee chromosome 2B, and its corresponding UBCS statistics has high values.
“we have observed that the genomic region distal to the HSA2 fusion site maps well to the near-telomeric region of chimpanzee chromosome 2B, and thus the corresponding UBCS statistics has high values (Fig. 1).”
From Revised time estimation of the ancestral human chromosome 2 fusion (2022) · cites this paper as [29]
The passages on genome-wide maps describe how the UCSC browser locates clones and markers on the human genome assembly; the Conclusion figures discuss chromosome 17 (pp. not specified). Searches for the HSA2 fusion site, chimpanzee chromosome 2B, and UBCS found no passage addressing the claimed mapping or statistic. (LLM, conf=0.76)
Experimental — accuracy not yet measuredHematologic phenotypes were examined at more than 7 weeks of age to avoid inter-individual variation.
“Hematologic phenotypes of a balanced mix of male and female mice for all models were examined at more than 7 weeks of age to avoid inter-individual variation42.”
From Genetic dissection of the α-globin super-enhancer in vivo (2016) · cites this paper as [42]
The 'Tracks Based on Homology with Other Species' section discusses mouse genome sequence alignments, not hematologic testing in mice. Searches for hematologic phenotypes, the seven-week age threshold, and inter-individual variation found no passage addressing the claim in our copy. (LLM, conf=0.76)
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- Authors
- Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D.
- Affiliations
- Howard Hughes Medical Institute (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2002-05-16
- Volume
- 12
- Issue
- 6
- Pages
- 996-1006
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC186604
- OpenAlex
- W2128016314
- Cited by
- 10,400
- References
- 41
- Citations by year
- 2026: 174 · 2025: 366 · 2024: 686 · 2023: 771 · 2022: 765 · 2021: 828 · 2020: 714 · 2019: 677 · 2018: 594 · 2017: 526 · 2016: 530 · 2015: 522 · 2014: 461 · 2013: 449 · 2012: 362
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Genome Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Energy (FG0399ER62849)
- National Human Genome Research Institute (P41HG002371, 1P41 HG 02371-01)
- 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 › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- UCSC Genome Browser, expressed sequence tags, gene prediction, cross-species homology, single nucleotide polymorphisms, sequence-tagged sites, MySQL
- MeSH terms
- California, Database Management Systems, Genes, Humans, RNA, Messenger, Sequence Homology, Nucleic Acid, Software, Universities, Gene Expression, Genome, Human, Databases, Genetic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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