Nucleic Acids Research, 2005, Vol. 33, Database issue D454-D458
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
The UCSC Proteome Browser
Center for Biomolecular Science and Engineering, School of Engineering and 1 Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA and 2 Sperling Biomedical Foundation, Eugene, OR 97405, USA
* To whom correspondence should be addressed. Tel: +1 831 459 5692; Fax: +1 831 459 1809; Email: fanhsu{at}soe.ucsc.edu
Received August 13, 2004; Revised and Accepted October 14, 2004
The University of California Santa Cruz (UCSC) Proteome Browser provides a wealth of protein information presented in graphical images and with links to other protein-related Internet sites. The Proteome Browser is tightly integrated with the UCSC Genome Browser. For the first time, Genome Browser users have both the genome and proteome worlds at their fingertips simultaneously. The Proteome Browser displays tracks of protein and genomic sequences, exon structure, polarity, hydrophobicity, locations of cysteine and glycosylation potential, Superfamily domains and amino acids that deviate from normal abundance. Histograms show genome-wide distribution of protein properties, including isoelectric point, molecular weight, number of exons, InterPro domains and cysteine locations, together with specific property values of the selected protein. The Proteome Browser also provides links to gene annotations in the Genome Browser, the Known Genes details page and the Gene Sorter; domain information from Superfamily, InterPro and Pfam; three-dimensional structures at the Protein Data Bank and ModBase; and pathway data at KEGG, BioCarta/CGAP and BioCyc. As of August 2004, the Proteome Browser is available for human, mouse and rat proteomes. The browser may be accessed from any Known Genes details page of the Genome Browser at http://genome.ucsc.edu. A user's guide is also available on this website.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  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]
|
|
|
|
|
|
R. M. Kuhn, D. Karolchik, A. S. Zweig, T. Wang, K. E. Smith, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, M. Pheasant, et al. The UCSC Genome Browser Database: update 2009 Nucleic Acids Res., January 1, 2009; 37(suppl_1): D755 - D761. [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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
A. G. Jegga, S. Gowrisankar, J. Chen, and B. J. Aronow PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease Nucleic Acids Res., January 12, 2007; 35(suppl_1): D700 - D706. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. A. Drake and P. Ping Thematic review series: Systems Biology Approaches to Metabolic and Cardiovascular Disorders. Proteomics approaches to the systems biology of cardiovascular diseases J. Lipid Res., January 1, 2007; 48(1): 1 - 8. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Hsu, W. J. Kent, H. Clawson, R. M. Kuhn, M. Diekhans, and D. Haussler The UCSC Known Genes Bioinformatics, May 1, 2006; 22(9): 1036 - 1046. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Kimura, A. Wakamatsu, Y. Suzuki, T. Ota, T. Nishikawa, R. Yamashita, J.-i. Yamamoto, M. Sekine, K. Tsuritani, H. Wakaguri, et al. Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes Genome Res., January 1, 2006; 16(1): 55 - 65. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. S. Hinrichs, D. Karolchik, R. Baertsch, G. P. Barber, G. Bejerano, H. Clawson, M. Diekhans, T. S. Furey, R. A. Harte, F. Hsu, et al. The UCSC Genome Browser Database: update 2006 Nucleic Acids Res., January 1, 2006; 34(suppl_1): D590 - D598. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Karchin, M. Diekhans, L. Kelly, D. J. Thomas, U. Pieper, N. Eswar, D. Haussler, and A. Sali LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources Bioinformatics, June 15, 2005; 21(12): 2814 - 2820. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. C. Lathe, M. E. Mangan, D. Karolchik, W. J. Kent, and D. Haussler Integrating Genomic Information through the UCSC Genome Browser Am. Assoc. Cancer Res. Educ. Book, April 1, 2005; 2005(1): 3 - 6. [Full Text] [PDF]
|
|