Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks
- Equal contributors
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
BMC Bioinformatics 2010, 11:392 doi:10.1186/1471-2105-11-392Published: 22 July 2010
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.
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.
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.