The UCSC Proteome Browser

Abstract

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.

Figure 1

This Proteome Browser tracks display sample shows the tracks of human protein CLOC_HUMAN in DNA mode that display both the protein and genomic sequences. As the corresponding mRNA is a negative strand, the DNA sequence and its complementary coding sequence are both shown. On the exon track, a part of the 2nd and 3rd exons is shown. The start of a Superfamily domain, Helix–loop–helix DNA-binding domain, is shown by the yellow bar. In this particular protein, the amino acid glutamine (Q) is flagged to indicate that it is present in a higher-than-average percentage.

Figure 2

The Proteome Browser property histograms sample shows that this protein has high molecular weight and a large number of exons. It has four InterPro domains and an unusually high concentration of glutamine.

Figure 3

This example shows the web links to UCSC Genome Browser, Known Gene details page and Gene Sorter; InterPro and Pfam domains; predicted 3D structure by ModBase; and pathways from BioCarta and KEGG.