International Journal of Data Mining and Bioinformatics
Quasi-bicliques: Complexity and Binding Pairs
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
International Journal of Data Mining and Bioinformatics
Efficient layered density-based clustering of categorical data
Journal of Biomedical Informatics
Modeling Protein Interacting Groups by Quasi-Bicliques: Complexity, Algorithm, and Application
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Near optimal solutions for maximum quasi-bicliques
COCOON'10 Proceedings of the 16th annual international conference on Computing and combinatorics
Information Sciences: an International Journal
Applying power graph analysis to weighted graphs
ECIR'12 Proceedings of the 34th European conference on Advances in Information Retrieval
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Motivation: Much research has been dedicated to large-scale protein interaction networks including the analysis of scale-free topologies, network modules and the relation of domain–domain to protein–protein interaction networks. Identifying locally significant proteins that mediate the function of modules is still an open problem. Method: We use a layered clustering algorithm for interaction networks, which groups proteins by the similarity of their direct neighborhoods. We identify locally significant proteins, called mediators, which link different clusters. We apply the algorithm to a yeast network. Results: Clusters and mediators are organized in hierarchies, where clusters are mediated by and act as mediators for other clusters. We compare the clusters and mediators to known yeast complexes and find agreement with precision of 71% and recall of 61%. We analyzed the functions, processes and locations of mediators and clusters. We found that 55% of mediators to a cluster are enriched with a set of diverse processes and locations, often related to translocation of biomolecules. Additionally, 82% of clusters are enriched with one or more functions. The important role of mediators is further corroborated by a comparatively higher degree of conservation across genomes. We illustrate the above findings with an example of membrane protein translocation from the cytoplasm to the inner nuclear membrane. Availability: All software is freely available under Supplementary information. Contact: williama@biotec.tu-dresden.de Supplementary information: http://www.cse.yorku.ca/billa/MODULARPIN/