The UCSC Known Genes
Top Cited Papers
Open Access
- 24 February 2006
- journal article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 22 (9) , 1036-1046
- https://doi.org/10.1093/bioinformatics/btl048
Abstract
The University of California Santa Cruz (UCSC) Known Genes dataset is constructed by a fully automated process, based on protein data from Swiss-Prot/TrEMBL (UniProt) and the associated mRNA data from Genbank. The detailed steps of this process are described. Extensive cross-references from this dataset to other genomic and proteomic data were constructed. For each known gene, a details page is provided containing rich information about the gene, together with extensive links to other relevant genomic, proteomic and pathway data. As of July 2005, the UCSC Known Genes are available for human, mouse and rat genomes. The Known Genes serves as a foundation to support several key programs: the Genome Browser, Proteome Browser, Gene Sorter and Table Browser offered at the UCSC website. All the associated data files and program source code are also available. They can be accessed at http://genome.ucsc.edu. The genomic coverage of UCSC Known Genes, RefSeq, Ensembl Genes, H-Invitational and CCDS is analyzed. Although UCSC Known Genes offers the highest genomic and CDS coverage among major human and mouse gene sets, more detailed analysis suggests all of them could be further improved.Keywords
This publication has 15 references indexed in Scilit:
- A highly sensitive selection method for directed evolution of homing endonucleasesNucleic Acids Research, 2005
- Exploring relationships and mining data with the UCSC Gene Sorter: Figure 1.Genome Research, 2005
- The Universal Protein Resource (UniProt)Nucleic Acids Research, 2004
- GenBankNucleic Acids Research, 2004
- The UCSC Proteome BrowserNucleic Acids Research, 2004
- NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteinsNucleic Acids Research, 2004
- The UCSC Table Browser data retrieval toolNucleic Acids Research, 2004
- The UCSC Genome Browser DatabaseNucleic Acids Research, 2003
- The Human Genome Browser at UCSCGenome Research, 2002
- The Protein Data BankNucleic Acids Research, 2000