Protein complex prediction via improved verification methods using constrained domain-domain matching
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概要
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In the field of functional genomics, identifying protein complexes within large-scale protein-protein interaction networks is one of the central research objectives due to limited availability of known protein complexes. Many approaches such as MCL and MCODE have been developed, and enabled researchers to detect protein complexes from protein-protein interaction networks. However, structural constraints of proteins have not been taken into consideration, and as a result, incorrect proteins were often extracted in predicted complexes. In order to prevent generation of too many erroneous complexes, Ozawa et al. proposed a verification method of protein complexes by introducing a constraint that a domain interacts with at most one other domain. In this technical report, we propose an improved integer programming-based method based on the idea that a candidate complex should not be divided into many small complexes. Furthermore, we enhance this method by combining with maximal components and extreme sets in graph theory. Comparison with the method by Ozawa et al. is conducted to show the advantage of our methods. The results suggest that the proposed methods outperform their method.
- 2012-03-21
著者
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Morihiro Hayashida
Bioinformatics Center Institute For Chemical Research Kyoto University
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Hiroshi Nagamochi
Department Of Applied Mathematics And Physics Kyoto University
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Tatsuya Akutsu
Bioinformatics Center Institute For Chemical Research Kyoto University
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Jose Nacher
Department Of Complex And Intelligent Systems Future University-hakodate
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Yang Zhao
Bioinformatics Center Institute For Chemical Research Kyoto University
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Hiroshi Nagamochi
Department Of Applied Mathematics And Physics Graduate School Of Informatics Kyoto University
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