Journal Article

Viewing cancer genes from co-evolving gene modules

Jing Zhu, Hui Xiao, Xiaopei Shen, Jing Wang, Jinfeng Zou, Lin Zhang, Da Yang, Wencai Ma, Chen Yao, Xue Gong, Min Zhang, Yang Zhang and Zheng Guo

in Bioinformatics

Volume 26, issue 7, pages 919-924
Published in print April 2010 | ISSN: 1367-4803
Published online February 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq055
Viewing cancer genes from co-evolving gene modules

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Motivation: Studying the evolutionary conservation of cancer genes can improve our understanding of the genetic basis of human cancers. Functionally related proteins encoded by genes tend to interact with each other in a modular fashion, which may affect both the mode and tempo of their evolution.

Results: In the human PPI network, we searched for subnetworks within each of which all proteins have evolved at similar rates since the human and mouse split. Identified at a given co-evolving level, the subnetworks with non-randomly large sizes were defined as co-evolving modules. We showed that proteins within modules tend to be conserved, evolutionarily old and enriched with housekeeping genes, while proteins outside modules tend to be less-conserved, evolutionarily younger and enriched with genes expressed in specific tissues. Viewing cancer genes from co-evolving modules showed that the overall conservation of cancer genes should be mainly attributed to the cancer proteins enriched in the conserved modules. Functional analysis further suggested that cancer proteins within and outside modules might play different roles in carcinogenesis, providing a new hint for studying the mechanism of cancer.

Contact: guoz@ems.hrbmu.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  4313 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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