The UCSC Table Browser data retrieval tool

By Donna Karolchik, A. Hinrichs, Terrence S. Furey, Krishna M. Roskin, Charles W. Sugnet, David Haussler, W. James Kent. Nucleic Acids Res., 2004

2,397 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d474f3dae01847a98c06c849ec2a01482bff23b4

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Citations in the corpus

A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence (2008, methodology): “We took advantage of a multiplesequence alignment of 17 genomes (human, chimpanzee, macaque, mouse, rat, rabbit, dog, cow, armadillo, elephant, tenrec, opossum, chicken, frog, zebrafish, green spotted puffer, and fugu) obtained from the University of California Santa Cruz (UCSC) Genome Browser (15),”
Spatiotemporal analysis of human intestinal development at single-cell resolution (2021, positive): “Human hg38 reference genome Ensembl gene annotations were obtained using the UCSC Table Browser Tool (Karolchik et al., 2004).”
The UCSC Genome Browser (2003, neutral): “…application and a variety of other useful tools: BLAT ( Kent et al., 2002 ), for quickly mapping sequences to a genome assembly; the Table Browser ( Karolchik et al., 2004 ; Fujita et al., 2011 ), for viewing and manipulating the data underlying the Genome Browser; the Gene Sorter ( Kent et al.,…”
Dynamic regulation of nucleosome positioning in the human genome. (2008, neutral): “The Affymetrix probe ids were then mapped to UCSC genes (Hsu et al., 2006) using the mapping table provided by the UCSC Genome Table Browser (Karolchik et al., 2004).”
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq (2013, positive): “31 (29), the RepeatMasker (35) and SimpleRepeat (36) tracks from UCSC (37).”
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants (2011, methodology): “To perform enhancer enrichment analysis on sets of variants, tables of common array designs were obtained from the UCSC Table Browser (34) and lists were constructed of 1000 Genomes SNPs segregating in each of the three pilot populations, as well as all SNPs in the database.”
The UCSC Genome Browser database: 2023 update (2022, neutral): “Nearly all data is available for extraction via bulk download, public MySQL server, RESTful API (10) or the Table Browser (11).”
The UCSC Genome Browser Database: update 2009 (2008, methodology): “All data are freely available via the Genome Browser and Table Browser interfaces, and may be downloaded in bulk at http://hgdown-load.cse.ucsc.edu.”
Promoter features related to tissue specificity as measured by Shannon entropy (2005, methodology): “The Q-based analyses of TATA box and initiator elements used genomic locations of DoTS genes on UCSC Golden Path release mm3 [60,61] to identify gene names.”
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. (2008, background): “edu) (Kent et al. 2002; Karolchik et al. 2004), such that sites were considered overlapping if there was at least 1 bp in common between the binding regions, which average ∼1000 bp in length.”