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ModuleSearch: finding functional modules in a protein–protein interaction network

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  • Guangyu Cui
  • Rojan Shrestha
  • Kyungsook Han

Abstract

Many biological processes are performed by a group of proteins rather than by individual proteins. Proteins involved in the same biological process often form a densely connected sub-graph in a protein–protein interaction network. Therefore, finding a dense sub-graph provides useful information to predict the function or protein complex of uncharacterised proteins in the sub-graph. We developed a heuristic algorithm that finds functional modules in a protein–protein interaction network and visualises the modules. The algorithm has been implemented in a platform-independent, standalone program called ModuleSearch. In an interaction network of yeast proteins, ModuleSearch found 366 overlapping modules. Of the modules, 71% have a function shared by more than half the proteins in the module and 58% have a function shared by all proteins in the module. Comparison of ModuleSearch with other programs shows that ModuleSearch finds more sub-graphs than most other programs, yet a higher proportion of the sub-graphs correspond to known functional modules. ModuleSearch and sample data are freely available to academics at http://bclab.inha.ac.kr/ModuleSearch.

Suggested Citation

  • Guangyu Cui & Rojan Shrestha & Kyungsook Han, 2012. "ModuleSearch: finding functional modules in a protein–protein interaction network," Computer Methods in Biomechanics and Biomedical Engineering, Taylor & Francis Journals, vol. 15(7), pages 691-699.
    • Handle: RePEc:taf:gcmbxx:v:15:y:2012:i:7:p:691-699
    DOI: 10.1080/10255842.2011.555404
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