title: Subpathway-GMir: identifying miRNA-mediated metabolic subpathways by integrating condition-specific genes, microRNAs, and pathway topologies.
abstract: MicroRNAs (miRNAs) regulate disease-relevant metabolic pathways. However, most current pathway identification methods fail to consider miRNAs in addition to genes when analyzing pathways. We developed a powerful method called Subpathway-GMir to construct miRNA-regulated metabolic pathways and to identify miRNA-mediated subpathways by considering condition-specific genes, miRNAs, and pathway topologies. We used Subpathway-GMir to analyze two liver hepatocellular carcinomas (LIHC), one stomach adenocarcinoma (STAD), and one type 2 diabetes (T2D) data sets. Results indicate that Subpathway-GMir is more effective in identifying phenotype-associated metabolic pathways than other methods and our results are reproducible and robust. Subpathway-GMir provides a flexible platform for identifying abnormal metabolic subpathways mediated by miRNAs, and may help to clarify the roles that miRNAs play in a variety of diseases. The Subpathway-GMir method has been implemented as a freely available R package.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Li
authors.initials: L
authors.lastname: Feng
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Xu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Yunpeng
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Zeguo
authors.initials: Z
authors.lastname: Sun
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Junwei
authors.initials: J
authors.lastname: Han
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Chunlong
authors.initials: C
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Haixiu
authors.initials: H
authors.lastname: Yang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Desi
authors.initials: D
authors.lastname: Shang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Su
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Xinrui
authors.initials: X
authors.lastname: Shi
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Shang
authors.initials: S
authors.lastname: Li
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.|Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.
authors.forename: Chunquan
authors.initials: C
authors.lastname: Li
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
authors.forename: Xia
authors.initials: X
authors.lastname: Li
mesh_terms: D000818:Animals; D006801:Humans; D053858:Metabolic Networks and Pathways; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D008957:Models, Genetic; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger
keywords: cancer; mRNA; microRNA; pathway identification; regulation