title: Viewing cancer genes from co-evolving gene modules.
abstract: 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.
authors.affiliation: 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.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhu
authors.forename: Hui
authors.initials: H
authors.lastname: Xiao
authors.forename: Xiaopei
authors.initials: X
authors.lastname: Shen
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Zou
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
authors.forename: Da
authors.initials: D
authors.lastname: Yang
authors.forename: Wencai
authors.initials: W
authors.lastname: Ma
authors.forename: Chen
authors.initials: C
authors.lastname: Yao
authors.forename: Xue
authors.initials: X
authors.lastname: Gong
authors.forename: Min
authors.initials: M
authors.lastname: Zhang
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.forename: Zheng
authors.initials: Z
authors.lastname: Guo
mesh_terms: 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*
chemical_list: D009363:Neoplasm Proteins