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Dense Module Enumeration in Biological Networks

  • Koji Tsuda
  • Elisabeth Georgii
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 939)

Abstract

Automatic discovery of functional complexes from protein interaction data is a rewarding but challenging problem. While previous approaches use approximations to extract dense modules, our approach exactly solves the problem of dense module enumeration. Furthermore, constraints from additional information sources such as gene expression and phenotype data can be integrated, so we can systematically detect dense modules with interesting profiles. Given a weighted protein interaction network, our method discovers all protein sets that satisfy a user-defined minimum density threshold. We employ a reverse search strategy, which allows us to exploit the density criterion in an efficient way.

Key words

Protein complex Dense module enumeration Reverse search Gene expression Protein interaction 

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.AIST Computational Biology Research CenterTokyoJapan
  2. 2.JST ERATO Minato ProjectSapporoJapan
  3. 3.School of ScienceHelsinki Institute for Information Technology HIIT Aalto UniversityAaltoFinland

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