title: Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks.
abstract: BACKGROUND
  Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regions.
  
  
  RESULTS
  Here, we weighted edges of a human protein interaction network and a transcriptional regulatory network to construct an integrated network, and introduce a probabilistic model and a bipartite graph framework to exploit human co-regulated modules and uncover their specific features in packaging different biological entities (genes, protein complexes or metabolic pathways). Finally, we identified 96 human co-regulated modules based on this method, and evaluate its effectiveness by comparing it with four other methods.
  
  
  CONCLUSIONS
  Dysfunctions in co-regulated interactions often occur in the development of cancer. Therefore, we focussed on an example co-regulated module and found that it could integrate a number of cancer-related genes. This was extended to causal dysfunctions of some complexes maintained by several physically interacting proteins, thus coordinating several metabolic pathways that directly underlie cancer.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Hei Longjiang Province, China. chenlina_2004@yahoo.com.cn
authors.forename: Lina
authors.initials: L
authors.lastname: Chen
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.forename: Liangcai
authors.initials: L
authors.lastname: Zhang
authors.forename: Wan
authors.initials: W
authors.lastname: Li
authors.forename: Qian
authors.initials: Q
authors.lastname: Wang
authors.forename: Yukui
authors.initials: Y
authors.lastname: Shang
authors.forename: Yuehan
authors.initials: Y
authors.lastname: He
authors.forename: Weiming
authors.initials: W
authors.lastname: He
authors.forename: Xu
authors.initials: X
authors.lastname: Li
authors.forename: Jingxie
authors.initials: J
authors.lastname: Tai
authors.forename: Xia
authors.initials: X
authors.lastname: Li
mesh_terms: D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D006801:Humans; D053858:Metabolic Networks and Pathways; D008957:Models, Genetic; D015233:Models, Statistical; D009369:Neoplasms / Q000235:genetics; D011506:Proteins / Q000378:metabolism*
chemical_list: D011506:Proteins