Viewing cancer genes from co-evolving gene modules.
BACKGROUND
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.
Zhu
Jing
J
Bioinformatics Centre and Key Laboratory for NeuroInfomation of the Education Ministry of China, School of Life Science, University of Electronic Science and Technology of China, Chengdu 610054, China.
Xiao
Hui
H
Shen
Xiaopei
X
Wang
Jing
J
Zou
Jinfeng
J
Zhang
Lin
L
Yang
Da
D
Ma
Wencai
W
Yao
Chen
C
Gong
Xue
X
Zhang
Min
M
Zhang
Yang
Y
Guo
Zheng
Z
D000818:Animals; D053263:Gene Regulatory Networks / Q000235:genetics*; D052138:Genes, Neoplasm; D023281:Genomics / Q000379:methods*; D006801:Humans; D009363:Neoplasm Proteins / Q000235:genetics; D009369:Neoplasms / Q000235:genetics*
D009363:Neoplasm Proteins