First Proteomic Exploration of Protein-Encoding Genes on Chromosome 1 in Human Liver, Stomach, and Colon

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• 作者：Songfeng Wu ; Ning Li ; Jie Ma ; Huali Shen ; Dahai Jiang ; Cheng Chang ; Chengpu Zhang ; Liwei Li ; Hongxing Zhang ; Jing Jiang ; Zhongwei Xu ; Lingyan Ping ; Tao Chen ; Wei Zhang ; Tao Zhang ; Xiaohua Xing ; Tailong Yi ; Yanchang Li ; Fengxu Fan ; Xiaoqian Li ; Fan Zhong ; Quanhui Wang ; Yang Zhang ; Bo Wen ; Guoquan Yan ; Liang Lin ; Jun Yao ; Zhilong Lin ; Feifei Wu ; Liqi Xie ; Hongxiu Yu ; Mingqi Liu ; Haojie Lu ; Hong Mu ; Dong Li ; Weimin Zhu ; Bei Zhen ; Xiaohong Qian ; Jun Qin ; Siqi Liu ; Pengyuan Yang ; Yunping Zhu ; Ping Xu ; Fuchu He
• 刊名：Journal of Proteome Research
• 出版年：2013
• 出版时间：January 4, 2013
• 年：2013
• 卷：12
• 期：1
• 页码：67-80
• 全文大小：946K
• 年卷期：v.12,no.1(January 4, 2013)
• ISSN：1535-3907

文摘

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/).

Keywords:

proteome; chromosome; C-HPP; coexpression; data visualization