Development and implementation of an algorithm for detection of protein complexes in large interaction networks.

BMC Bioinformatics
Md Altaf-Ul-AminShigehiko Kanaya

Abstract

After complete sequencing of a number of genomes the focus has now turned to proteomics. Advanced proteomics technologies such as two-hybrid assay, mass spectrometry etc. are producing huge data sets of protein-protein interactions which can be portrayed as networks, and one of the burning issues is to find protein complexes in such networks. The enormous size of protein-protein interaction (PPI) networks warrants development of efficient computational methods for extraction of significant complexes. This paper presents an algorithm for detection of protein complexes in large interaction networks. In a PPI network, a node represents a protein and an edge represents an interaction. The input to the algorithm is the associated matrix of an interaction network and the outputs are protein complexes. The complexes are determined by way of finding clusters, i. e. the densely connected regions in the network. We also show and analyze some protein complexes generated by the proposed algorithm from typical PPI networks of Escherichia coli and Saccharomyces cerevisiae. A comparison between a PPI and a random network is also performed in the context of the proposed algorithm. The proposed algorithm makes it possible to detect clusters of ...Continue Reading

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Citations

Dec 7, 2013·Interdisciplinary Sciences, Computational Life Sciences·True PriceYoung-Rae Cho
Aug 11, 2011·Computer Methods in Biomechanics and Biomedical Engineering·Guangyu CuiKyungsook Han
Jul 23, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Min WuLimsoon Wong
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May 14, 2009·BMC Bioinformatics·Feng LuoRichard H Scheuermann
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Nov 8, 2006·BMC Bioinformatics·Sylvain Brohée, Jacques van Helden
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Methods Mentioned

BETA
two hybrid

Software Mentioned

Python
java
MathType

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