A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles

Background: Many research results show that the biological systems are composed of functional modules. Members in the same module usually have common functions. This is useful information to understand how biological systems work. Therefore, detecting functional modules is an important research topic in the post-genome era. One of functional module detecting methods is to find dense regions in Protein-Protein Interaction (PPI) networks. Most of current methods neglect confidence-scores of interactions, and pay little attention on using gene expression data to improve their results. Results: In this paper, we propose a novel hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles, and we name it HUNTER. Our method not only can extract functional modules from a weighted PPI network, but also use gene expression data as optional input to increase the quality of outcomes. Using HUNTER on yeast data, we found it can disco...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Chia-Hao Chin, Shu-Hwa Chen, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin
• Keywords: Biological Systems, BMCBI 2010, Functional Modules, Gene Expression Data