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Bioinformatics Advance Access originally published online on February 24, 2006
Bioinformatics 2006 22(9):1036-1046; doi:10.1093/bioinformatics/btl048
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
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The UCSC Known Genes

Fan Hsu 1,*, W. James Kent 1, Hiram Clawson 1, Robert M. Kuhn 1, Mark Diekhans 1 and David Haussler 2

1 Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz Santa Cruz, CA 95064, USA
2 Howard Hughes Medical Institute, University of California Santa Cruz Santa Cruz, CA 95064, USA

*To whom correspondence should be addressed.

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.

Contact: fanhsu{at}soe.ucsc.edu

Received on September 9, 2005; revised on January 23, 2006; accepted on February 7, 2006

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