T
he launch of t
he Chromosome-Centric Human Proteome Project provides an opportunity to gain insight into t
he human proteome. T
he Chinese Human Chromosome Proteome Consortium has initiated proteomic exploration of protein-encoding genes on human chromosomes 1, 8, and 20. Collaboration within t
he consortium has generated a compre
hensive proteome data set using normal and carcinomatous tissues from human liver, stomach, and colon and 13 cell lines originating in t
hese organs. We identified 12,101 proteins (59.8% coverage against Swiss-Prot human entries) with a protein false discovery rate of less than 1%. On chromosome 1, 1,252 proteins map
ping to 1,227 genes, representing 60.9% of Swiss-Prot entries, were identified; however, 805 proteins remain unidentified, suggesting that analysis of more diverse samples using more advanced proteomic technologies is required. Genes encoding t
he unidentified proteins were concentrated in seven blocks, located at p36, q12-21, and q42-44, partly consistent with correlation of t
hese blocks with cancers of t
he liver, stomach, and colon. Combined transcriptome, proteome, and cofunctionality analyses confirmed 23 coexpression clusters containing 165 genes. Biological information, 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 t
he Chinese Chromosome-Centric Human Proteome Database (
http://proteomeview.hupo.org.cn/chromosome/).
Keywords:
proteome; chromosome; C-HPP; coexpression; data visualization