The UCSC Genome Browser Database

By Donna Karolchik, Robert Baertsch, Mark Diekhans, Terrence S. Furey, A. Hinrichs, Y. Lu, Krishna M. Roskin, M. Schwartz, Charles W. Sugnet, Daryl J. Thomas and 3 more. Nucleic Acids Res., 2003

2,234 citations recorded by the source corpus.

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/e049bd1ef18a0f1cdb45477d957393cf9ef41c6d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Andrej Sali
2. Ben M. Webb
3. David P. Bartel
4. John S. Mattick
5. David Haussler
6. Nikolaus Rajewsky
7. V. Narry Kim
8. Min-Yi Shen

In Plant Science

1. David Haussler
2. W. James Kent
3. Adam C. Siepel
4. Nikolaus Rajewsky
5. David P. Bartel
6. Robert M. Kuhn
7. John S. Mattick
8. Martin C. Frith

Citations in the corpus

• Processing of intronic microRNAs (2007, methodology): “However, more careful analysis revealed that a significant number of miRNAs are in the introns of TUs that are predicted or annotated to be protein-coding.”
• g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments (2007, methodology): “First, TFBS are found by matching TRANSFAC position-specific matrices using the program Match (20) on 1000-bp upstream regions, as provided by the UCSC genome database (21).”
• miRBase: microRNA sequences, targets and gene nomenclature (2005, background): “Distributed annotation system (DAS) sources provide easy access to miRNA genomic locations, and the data are available for viewing within the Ensembl (19) and UCSC browsers (20).”
• IL-33, an interleukin-1-like cytokine that signals via the IL-1 receptor-related protein ST2 and induces T helper type 2-associated cytokines. (2005, methodology): “…thologoushumanandmousesequenceswerededucedbysequenc-ingESTs(AL545605andBE915331,respectively);thecorrespondingmousegenewaslocatedwiththeUCSCGenomeBrowser(Karolchik et al., 2003), and the predicted genomic sequence was used to isolate a full-length cDNA by use of PCR from a mouse lung Marathon-Ready”
• Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. (2008, background): “A similar hp-siRNA biogenesis pathway has been reported in mouse oocytes (Tam et al. 2008; Watanabe et al. 2008) and in Drosophila (Czech et al. 2008; Ghildiyal et al. 2008; Kawamura et al. 2008; Okamura et al. 2008).”
• snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs (2005, background): “We thank the UCSC Genome Browser team, in particular Jim Kent, Dona Karolchik, Fan Hsu and Hiram Clawson, for their help in the building of the human sno/miRNA track.”
• The UCSC Genome Browser (2003, neutral): “Another tool on the Web site—the UCSC Table Browser—facilitates convenient access to the MySql database tables (Karolchik et al., 2003) underlying the Genome Browser annotations.”
• Genome-wide analysis of mammalian promoter architecture and evolution (2006, background): “and extracted positions of CpG islands from the UCSC Genome Browser databas”
• A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence (2008, methodology): “The 17-genome multiple alignment used in this study was obtained from the UCSC Genome Browser (multiple alignment files are available directly from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/ multiz17way/).”
• Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters (2012, methodology): “Coding (“CDS”), intergenic and promoter backgrounds were selected randomly from the corresponding region in the yeast genome, as annotated in the UCSC genome browser 36 .”
• The UCSC Table Browser data retrieval tool (2004, methodology): “The UCSC Table Browser data retrieval tool is built on top of the Genome Browser Database, a set of MySQL relational databases that each store sequence and annotation data for one genome assembly (1).”