Bioinformatics Advance Access originally published online on February 24, 2006
Bioinformatics 2006 22(9):1036-1046; doi:10.1093/bioinformatics/btl048
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The UCSC Known Genes
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
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  N. L. Barbosa-Morais, M. J. Dunning, S. A. Samarajiwa, J. F. J. Darot, M. E. Ritchie, A. G. Lynch, and S. Tavare A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data Nucleic Acids Res., November 18, 2009; (2009) gkp942v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Rhead, D. Karolchik, R. M. Kuhn, A. S. Hinrichs, A. S. Zweig, P. A. Fujita, M. Diekhans, K. E. Smith, K. R. Rosenbloom, B. J. Raney, et al. The UCSC genome browser database: update 2010 Nucleic Acids Res., November 11, 2009; (2009) gkp939v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Barski, R. Jothi, S. Cuddapah, K. Cui, T.-Y. Roh, D. E. Schones, and K. Zhao Chromatin poises miRNA- and protein-coding genes for expression Genome Res., October 1, 2009; 19(10): 1742 - 1751. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Han, X. Wu, W.-Y. Chung, T. Li, A. Nekrutenko, N. S. Altman, G. Chen, and H. Ma Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing PNAS, August 4, 2009; 106(31): 12741 - 12746. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Nam, M. Li, K. Choi, C. Balch, S. Kim, and K. P. Nephew MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression Nucleic Acids Res., July 1, 2009; 37(suppl_2): W356 - W362. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. C. Pang, M. E. Dinger, T. R. Mercer, L. Malquori, S. M. Grimmond, W. Chen, and J. S. Mattick Genome-Wide Identification of Long Noncoding RNAs in CD8+ T Cells J. Immunol., June 15, 2009; 182(12): 7738 - 7748. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. I. Sigurdsson, A. V. Smith, H. T. Bjornsson, and J. J. Jonsson HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination Genome Res., April 1, 2009; 19(4): 581 - 589. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Chelala, A. Khan, and N. R Lemoine SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms Bioinformatics, March 1, 2009; 25(5): 655 - 661. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Whitington, A. C. Perkins, and T. L. Bailey High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites Nucleic Acids Res., January 1, 2009; 37(1): 14 - 25. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Pieper, N. Eswar, B. M. Webb, D. Eramian, L. Kelly, D. T. Barkan, H. Carter, P. Mankoo, R. Karchin, M. A. Marti-Renom, et al. MODBASE, a database of annotated comparative protein structure models and associated resources Nucleic Acids Res., January 1, 2009; 37(suppl_1): D347 - D354. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. M. Muro, R. Herrington, S. Janmohamed, C. Frelin, M. A. Andrade-Navarro, and N. N. Iscove Identification of gene 3' ends by automated EST cluster analysis PNAS, December 23, 2008; 105(51): 20286 - 20290. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. G. Robertson, M. Bilenky, A. Tam, Y. Zhao, T. Zeng, N. Thiessen, T. Cezard, A. P. Fejes, E. D. Wederell, R. Cullum, et al. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding Genome Res., December 1, 2008; 18(12): 1906 - 1917. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. McLean and G. Bejerano Dispensability of mammalian DNA Genome Res., November 1, 2008; 18(11): 1743 - 1751. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. H. Kim, P. Saetrom, O. Snove Jr., and J. J. Rossi Cozzarelli Prize Winner: MicroRNA-directed transcriptional gene silencing in mammalian cells PNAS, October 21, 2008; 105(42): 16230 - 16235. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Burgess and Z. Yang Estimation of Hominoid Ancestral Population Sizes under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors Mol. Biol. Evol., September 1, 2008; 25(9): 1979 - 1994. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. D. Wall, M. P. Cox, F. L. Mendez, A. Woerner, T. Severson, and M. F. Hammer A novel DNA sequence database for analyzing human demographic history Genome Res., August 1, 2008; 18(8): 1354 - 1361. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Hellmann, Y. Mang, Z. Gu, P. Li, F. M. de la Vega, A. G. Clark, and R. Nielsen Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals Genome Res., July 1, 2008; 18(7): 1020 - 1029. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Fullwood, J. J. S. Tan, P. W. P. Ng, K. P. Chiu, J. Liu, C. L. Wei, and Y. Ruan The use of multiple displacement amplification to amplify complex DNA libraries Nucleic Acids Res., March 1, 2008; 36(5): e32 - e32. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Stephen, M. Pheasant, I. V. Makunin, and J. S. Mattick Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock Mol. Biol. Evol., February 1, 2008; 25(2): 402 - 408. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. R. Mercer, M. E. Dinger, S. M. Sunkin, M. F. Mehler, and J. S. Mattick Specific expression of long noncoding RNAs in the mouse brain PNAS, January 15, 2008; 105(2): 716 - 721. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Karolchik, R. M. Kuhn, R. Baertsch, G. P. Barber, H. Clawson, M. Diekhans, B. Giardine, R. A. Harte, A. S. Hinrichs, F. Hsu, et al. The UCSC Genome Browser Database: 2008 update Nucleic Acids Res., January 11, 2008; 36(suppl_1): D773 - D779. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Rice Annotation Project The Rice Annotation Project Database (RAP-DB): 2008 update Nucleic Acids Res., January 11, 2008; 36(suppl_1): D1028 - D1033. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Cutler, L. A. Marshall, N. Chin, H. Baribault, and P. D. Kassner Significant gene content variation characterizes the genomes of inbred mouse strains Genome Res., December 1, 2007; 17(12): 1743 - 1754. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. M. Koch, R. M. Andrews, P. Flicek, S. C. Dillon, U. Karaoz, G. K. Clelland, S. Wilcox, D. M. Beare, J. C. Fowler, P. Couttet, et al. The landscape of histone modifications across 1% of the human genome in five human cell lines Genome Res., June 1, 2007; 17(6): 691 - 707. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Rhesus Macaque Genome Sequencing and Analysis Cons, R. A. Gibbs, J. Rogers, M. G. Katze, R. Bumgarner, G. M. Weinstock, E. R. Mardis, K. A. Remington, R. L. Strausberg, J. C. Venter, et al. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome Science, April 13, 2007; 316(5822): 222 - 234. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. J. Cooper, N. D. Trinklein, L. Nguyen, and R. M. Myers Serum response factor binding sites differ in three human cell types Genome Res., February 1, 2007; 17(2): 136 - 144. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Tian, Z. Pan, and J. Y. Lee Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing Genome Res., February 1, 2007; 17(2): 156 - 165. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. S. Alioto U12DB: a database of orthologous U12-type spliceosomal introns Nucleic Acids Res., January 12, 2007; 35(suppl_1): D110 - D115. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. M. Kuhn, D. Karolchik, A. S. Zweig, H. Trumbower, D. J. Thomas, A. Thakkapallayil, C. W. Sugnet, M. Stanke, K. E. Smith, A. Siepel, et al. The UCSC genome browser database: update 2007 Nucleic Acids Res., January 12, 2007; 35(suppl_1): D668 - D673. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hiller, S. Nikolajewa, K. Huse, K. Szafranski, P. Rosenstiel, S. Schuster, R. Backofen, and M. Platzer TassDB: a database of alternative tandem splice sites Nucleic Acids Res., January 12, 2007; 35(suppl_1): D188 - D192. [Abstract] [Full Text] [PDF]
|
|