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Qualitative and Quantitative Expression Status of the Human Chromosome 20 Genes in Cancer Tissues and the Representative Cell Lines

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journal contribution
posted on 20.02.2016, 02:43 by Quanhui Wang, Bo Wen, Guangrong Yan, Junying Wei, Liqi Xie, Shaohang Xu, Dahai Jiang, Tingyou Wang, Liang Lin, Jin Zi, Ju Zhang, Ruo Zhou, Haiyi Zhao, Zhe Ren, Nengrong Qu, Xiaomin Lou, Haidan Sun, Chaoqin Du, Chuangbin Chen, Shenyan Zhang, Fengji Tan, Youqi Xian, Zhibo Gao, Minghui He, Longyun Chen, Xiaohang Zhao, Ping Xu, Yunping Zhu, Xingfeng Yin, Huali Shen, Yang Zhang, Jing Jiang, Chengpu Zhang, Liwei Li, Cheng Chang, Jie Ma, Guoquan Yan, Jun Yao, Haojie Lu, Wantao Ying, Fan Zhong, Qing-Yu He, Siqi Liu
Under the guidance of the Chromosome-centric Human Proteome Project (C-HPP),, we conducted a systematic survey of the expression status of genes located at human chromosome 20 (Chr.20) in three cancer tissues, gastric, colon, and liver carcinoma, and their representative cell lines. We have globally profiled proteomes in these samples with combined technology of LC–MS/MS and acquired the corresponding mRNA information upon RNA-seq and RNAchip. In total, 323 unique proteins were identified, covering 60% of the coding genes (323/547) in Chr.20. With regards to qualitative information of proteomics, we overall evaluated the correlation of the identified Chr.20 proteins with target genes of transcription factors or of microRNA, conserved genes and cancer-related genes. As for quantitative information, the expression abundances of Chr.20 genes were found to be almost consistent in both tissues and cell lines of mRNA in all individual chromosome regions, whereas those of Chr.20 proteins in cells are different from tissues, especially in the region of 20q13.33. Furthermore, the abundances of Chr.20 proteins were hierarchically evaluated according to tissue- or cancer-related distribution. The analysis revealed several cancer-related proteins in Chr.20 are tissue- or cell-type dependent. With integration of all the acquired data, for the first time we established a solid database of the Chr.20 proteome.