title: Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information.
abstract: In humans, despite the rapid increase in disease-associated gene discovery, a large proportion of disease-associated genes are still unknown. Many network-based approaches have been used to prioritize disease genes. Many networks, such as the protein-protein interaction (PPI), KEGG, and gene co-expression networks, have been used. Expression quantitative trait loci (eQTLs) have been successfully applied for the determination of genes associated with several diseases. In this study, we constructed an eQTL-based gene-gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining.
authors: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China ; School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China ; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
authors: Jin
authors: J
authors: Li
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China ; School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China.
authors: Limei
authors: L
authors: Wang
authors: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
authors: Maozu
authors: M
authors: Guo
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
authors: Ruijie
authors: R
authors: Zhang
authors: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
authors: Qiguo
authors: Q
authors: Dai
authors: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
authors: Xiaoyan
authors: X
authors: Liu
authors: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
authors: Chunyu
authors: C
authors: Wang
authors: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
authors: Zhixia
authors: Z
authors: Teng
authors: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
authors: Ping
authors: P
authors: Xuan
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
authors: Mingming
authors: M
authors: Zhang
keywords: AD, Alzheimer disease; Co-regulation network; Disease gene mining; GGCRN, gene–gene co-regulation network; HPRD, Human Protein Reference Database; KEGG, Kyoto Encyclopedia of Genes and Genomes; PPI, protein–protein interaction; Protein–protein interaction; RWR, random walk with restart; Random walk with restart; SNP, single-nucleotide polymorphism; eQTL; eQTLs, expression quantitative trait loci