Community structure detection for overlapping modules through mathematical programming in protein interaction networks
| Autor: | Songsong Liu, Aristotelis Kittas, Lazaros G. Papageorgiou, Sophia Tsoka, Laura Bennett |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Optimization
Saccharomyces cerevisiae Proteins Theoretical computer science Protein domain lcsh:Medicine Genetic Networks Saccharomyces cerevisiae Disjoint sets Biology Bioinformatics Escherichia coli Animals Humans Partition (number theory) Protein Interaction Maps lcsh:Science Multidisciplinary Systems Biology Escherichia coli Proteins lcsh:R Community structure Biology and Life Sciences Computational Biology Models Theoretical Complex network Genome Analysis Standard problem Rats Protein Interaction Networks Physical Sciences lcsh:Q Centrality Mathematics Algorithms Research Article |
| Zdroj: | PLoS ONE, Vol 9, Iss 11, p e112821 (2014) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | Community structure detection has proven to be important in revealing the underlying properties of complex networks. The standard problem, where a partition of disjoint communities is sought, has been continually adapted to offer more realistic models of interactions in these systems. Here, a two-step procedure is outlined for exploring the concept of overlapping communities. First, a hard partition is detected by employing existing methodologies. We then propose a novel mixed integer non linear programming (MINLP) model, known as OverMod, which transforms disjoint communities to overlapping. The procedure is evaluated through its application to protein-protein interaction (PPI) networks of the rat, E. coli, yeast and human organisms. Connector nodes of hard partitions exhibit topological and functional properties indicative of their suitability as candidates for multiple module membership. OverMod identifies two types of connector nodes, inter and intra-connector, each with their own particular characteristics pertaining to their topological and functional role in the organisation of the network. Inter-connector proteins are shown to be highly conserved proteins participating in pathways that control essential cellular processes, such as proliferation, differentiation and apoptosis and their differences with intra-connectors is highlighted. Many of these proteins are shown to possess multiple roles of distinct nature through their participation in different network modules, setting them apart from proteins that are simply 'hubs', i.e. proteins with many interaction partners but with a more specific biochemical role. |
| Databáze: | OpenAIRE |
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