title: First proteomic exploration of protein-encoding genes on chromosome 1 in human liver, stomach, and colon.
abstract: The launch of the Chromosome-Centric Human Proteome Project provides an opportunity to gain insight into the human proteome. The Chinese Human Chromosome Proteome Consortium has initiated proteomic exploration of protein-encoding genes on human chromosomes 1, 8, and 20. Collaboration within the consortium has generated a comprehensive proteome data set using normal and carcinomatous tissues from human liver, stomach, and colon and 13 cell lines originating in these 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 mapping 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 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, 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 the Chinese Chromosome-Centric Human Proteome Database ( http://proteomeview.hupo.org.cn/chromosome/ ).
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China.
authors.forename: Songfeng
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authors.forename: Jie
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authors.forename: Yanchang
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authors.forename: Fengxu
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authors.forename: Xiaoqian
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authors.forename: Fan
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authors.forename: Quanhui
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authors.lastname: Zhang
authors.forename: Bo
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authors.forename: Guoquan
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authors.lastname: Yan
authors.forename: Liang
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authors.lastname: Lin
authors.forename: Jun
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authors.lastname: Yao
authors.forename: Zhilong
authors.initials: Z
authors.lastname: Lin
authors.forename: Feifei
authors.initials: F
authors.lastname: Wu
authors.forename: Liqi
authors.initials: L
authors.lastname: Xie
authors.forename: Hongxiu
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authors.lastname: Yu
authors.forename: Mingqi
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authors.lastname: Liu
authors.forename: Haojie
authors.initials: H
authors.lastname: Lu
authors.forename: Hong
authors.initials: H
authors.lastname: Mu
authors.forename: Dong
authors.initials: D
authors.lastname: Li
authors.forename: Weimin
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authors.lastname: Zhu
authors.forename: Bei
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authors.lastname: Zhen
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Qian
authors.forename: Jun
authors.initials: J
authors.lastname: Qin
authors.forename: Siqi
authors.initials: S
authors.lastname: Liu
authors.forename: Pengyuan
authors.initials: P
authors.lastname: Yang
authors.forename: Yunping
authors.initials: Y
authors.lastname: Zhu
authors.forename: Ping
authors.initials: P
authors.lastname: Xu
authors.forename: Fuchu
authors.initials: F
authors.lastname: He
mesh_terms: D002878:Chromosomes, Human, Pair 1 / Q000235:genetics / Q000378:metabolism; D003106:Colon / Q000378:metabolism; D016208:Databases, Factual; D030562:Databases, Protein; D005753:Gastric Mucosa / Q000378:metabolism; D015870:Gene Expression; D015894:Genome, Human; D016045:Human Genome Project; D006801:Humans; D008099:Liver / Q000378:metabolism; D011506:Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D020543:Proteome
chemical_list: D011506:Proteins; D020543:Proteome