NWE: Node-Weighted Expansion for protein complex prediction using random walk distances

Osamu Maruyama, Ayaka Chihara

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

Protein complexes are important entities to organize various biological systems. However, they are still limited in availability. Thus, it is a challenging problem to predict protein complexes computationally from existing genome-wide data sets, like protein-protein interaction (PPI) networks. In this paper, we propose an efficient algorithm for predicting protein complexes by random walking on a PPI network. The algorithm is designed based on the method of node-weighted expansion of a cluster, which simulates a random walk with restarts with the weighted nodes of the cluster. We have validated the biological significance of the results using curated complexes in the CYC2008 database. We have compared our method to a clustering-based method, MCL, and a repeated random walk-based method, RRW, and found that our algorithm outperforms the other algorithms.

Original languageEnglish
Title of host publicationProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Pages590-594
Number of pages5
DOIs
Publication statusPublished - 2010
Event2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010 - Hong Kong, China
Duration: Dec 18 2010Dec 21 2010

Publication series

NameProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010

Other

Other2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
CountryChina
CityHong Kong
Period12/18/1012/21/10

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Informatics

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    Maruyama, O., & Chihara, A. (2010). NWE: Node-Weighted Expansion for protein complex prediction using random walk distances. In Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010 (pp. 590-594). [5706634] (Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010). https://doi.org/10.1109/BIBM.2010.5706634