title: Identifying functional modules for coronary artery disease by a prior knowledge-based approach.
abstract: Until recently, the underlying genetic mechanisms for coronary artery disease (CAD) have been largely unknown, with just a list of genes identified accounting for very little of the disease in the population. Hence, a systematic dissection of the sophisticated interplays between these individual disease genes and their functional involvements becomes essential. Here, we presented a novel knowledge-based approach to identify the functional modules for CAD. First, we selected 266 disease genes in CADgene database as the initial seed genes, and used PPI knowledge as a guide to expand these genes into a CAD-specific gene network. Then, we used Newman's algorithm to decompose the primary network into 14 compact modules with high modularity. By analysis of these modules, we further identified 114 hub genes, all either directly or indirectly associated with CAD. Finally, by functional analysis of these modules, we revealed several novel pathogenic mechanisms for CAD (for examples, some yet rarely concerned like peptide YY receptor activity, Fc gamma R-mediated phagocytosis and actin cytoskeleton regulation etc.).
authors.affiliation: Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China.
authors.forename: Haoli
authors.initials: H
authors.lastname: Li
authors.affiliation: Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China; Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zuo
authors.affiliation: Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Ouyang
authors.affiliation: Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China.
authors.forename: Meihua
authors.initials: M
authors.lastname: Lin
authors.affiliation: Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China; Department of Statistical Sciences, School of Mathematics and Computational Science, Sun Yat-sen University, Guangzhou 510080, China.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: Department of Internal Cardiovascular Medicine, Maoming People's Hospital, Maoming 525000, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Liang
authors.affiliation: Department of Internal Cardiovascular Medicine, Maoming People's Hospital, Maoming 525000, China.
authors.forename: Shouqiang
authors.initials: S
authors.lastname: Zhong
authors.affiliation: Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, School of Public Health, Guangdong Medical College, Dongguan 523808, China; Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China; Department of Statistical Sciences, School of Mathematics and Computational Science, Sun Yat-sen University, Guangzhou 510080, China. Electronic address: raoshaoq@gdmc.edu.cn.
authors.forename: Shaoqi
authors.initials: S
authors.lastname: Rao
mesh_terms: D000465:Algorithms; D003324:Coronary Artery Disease / Q000235:genetics*; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease; D006801:Humans; D051188:Knowledge Bases; D058977:Molecular Sequence Annotation
keywords: CAD; Coronary artery disease; Data mining; GO; Gene Ontology; Gene annotation; Gene module; HPRD; Human Protein Reference Database; PPI; Protein interaction maps; Protein–protein interaction; VSMC; Vascular smooth muscle cell