DocumentCode :
1989480
Title :
Optimizing Flow-based Modularization by Iterative Centroid Search in Protein Interaction Networks
Author :
Cho, Young-Rae ; Hwang, Woochang ; Zhang, Aidong
Author_Institution :
State Univ. of New York at Buffalo, Buffalo
fYear :
2007
fDate :
14-17 Oct. 2007
Firstpage :
342
Lastpage :
349
Abstract :
The systematic analysis of protein-protein interactions is a fundamental step for understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks. However, current unreliable interaction data and complex connectivity of interaction networks have made it challenging. We propose a novel metric, called semantic interactivity, to measure the reliability of protein-protein interactions using gene ontology (GO) annotation data. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability to each edge as a weight. We present an iterative centroid search (ICES) algorithm for optimizing the flow-based modularization method and identifying functional modules in a weighted interaction network. It iteratively performs two procedures: centroid search and flow simulation. Our experimental results show that the accuracy of modules is enhanced during the iteration.
Keywords :
biochemistry; biology computing; cellular biophysics; genetics; graph theory; iterative methods; molecular biophysics; ontologies (artificial intelligence); proteins; cellular functions; cellular organization; cellular processes; flow simulation; flow-based modularization; functional modules; gene ontology annotation data; iterative centroid search; optimization; protein interaction networks; protein-protein interactions; semantic interactivity; weighted graph representation; weighted interaction network; Cellular networks; Clustering algorithms; Computer science; Density functional theory; Iterative algorithms; Iterative methods; Ontologies; Partitioning algorithms; Protein engineering; Voting;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on
Conference_Location :
Boston, MA
Print_ISBN :
978-1-4244-1509-0
Type :
conf
DOI :
10.1109/BIBE.2007.4375586
Filename :
4375586
Link To Document :
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