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Open Access Research article

Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks

Lina Chen1*, Hong Wang1, Liangcai Zhang1, Wan Li1, Qian Wang1, Yukui Shang1, Yuehan He1, Weiming He2, Xu Li1, Jingxie Tai1 and Xia Li1*

Author Affiliations

1 College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Hei Longjiang Province, China

2 Institute of Opto-electronics, Harbin Institute of Technology, Harbin, Hei Longjiang Province, China

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BMC Bioinformatics 2010, 11:392  doi:10.1186/1471-2105-11-392

Published: 22 July 2010

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.