title: DISCOVERY OF FUNCTIONAL AND DISEASE PATHWAYS BY COMMUNITY DETECTION IN PROTEIN-PROTEIN INTERACTION NETWORKS.
abstract: Advances in cellular, molecular, and disease biology depend on the comprehensive characterization of gene interactions and pathways. Traditionally, these pathways are curated manually, limiting their efficient annotation and, potentially, reinforcing field-specific bias. Here, in order to test objective and automated identification of functionally cooperative genes, we compared a novel algorithm with three established methods to search for communities within gene interaction networks. Communities identified by the novel approach and by one of the established method overlapped significantly (q < 0.1) with control pathways. With respect to disease, these communities were biased to genes with pathogenic variants in ClinVar (p ≪ 0.01), and often genes from the same community were co-expressed, including in breast cancers. The interesting subset of novel communities, defined by poor overlap to control pathways also contained co-expressed genes, consistent with a possible functional role. This work shows that community detection based on topological features of networks suggests new, biologically meaningful groupings of genes that, in turn, point to health and disease relevant hypotheses.
authors.affiliation: Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA, sw5@bcm.edu.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Wilson
authors.forename: Angela D
authors.initials: AD
authors.lastname: Wilkins
authors.forename: Chih-Hsu
authors.initials: CH
authors.lastname: Lin
authors.forename: Rhonald C
authors.initials: RC
authors.lastname: Lua
authors.forename: Olivier
authors.initials: O
authors.lastname: Lichtarge
mesh_terms: D000465:Algorithms; D020788:Bardet-Biedl Syndrome / Q000235:genetics; D001943:Breast Neoplasms / Q000235:genetics; D019295:Computational Biology; D004843:Epistasis, Genetic; D005260:Female; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease; D006801:Humans; D060066:Protein Interaction Maps / Q000235:genetics; D015211:Zellweger Syndrome / Q000235:genetics