The launch of the Chromosome-Centric Hu
man Proteome Project provides an opportunity to gain insight into the hu
man proteome. The Chinese Hu
man Chromosome Proteome Consortium has initiated proteomic exploration of protein-encoding genes on hu
man chromosomes 1, 8, and 20. Collaboration within the consortium has generated a comprehensive proteome data set using nor
mal and carcino
matous tissues from hu
man liver, sto
mach, and colon and 13 cell lines originating in these organs. We identified 12,101 proteins (59.8% coverage against Swiss-Prot hu
man entries) with a protein false discovery rate of less than 1%. On chromosome 1, 1,252 proteins
mapping to 1,227 genes, representing 60.9% of Swiss-Prot entries, were identified; however, 805 proteins re
main unidentified, suggesting that analysis of more diverse samples using more advanced proteomic technologies is required. Genes encoding the unidentified proteins were concentrated in seven blocks, located at p36, q12-21, and q42-44, partly consistent with correlation of these blocks with cancers of the liver, sto
mach, and colon. Combined transcriptome, proteome, and cofunctionality analyses confirmed 23 coexpression clusters containing 165 genes. Biological infor
mation, including chromosome structure, GC content, and protein coexpression pattern was analyzed using multilayered, circular visualization and tabular visualization. Details of data analysis and updates are available in the Chinese Chromosome-Centric Hu
man Proteome Database (
http://proteomeview.hupo.org.cn/chromosome/).
Keywords:
proteome; chromosome; C-HPP; coexpression; data visualization