G-M Li1, C-L Zhang, R-P Rui, B Sun, W Guo. 1. Department of Cardiology, Yidu Central Hospital of Weifang, Qingzhou, P.R. China. drguowei17@163.com.
Abstract
OBJECTIVE: This paper aims at screening the common differential genes of coronary atherosclerotic heart disease (CAD) and ischemic cardiomyopathy (ICM), and to conduct pathway analysis and protein-protein interaction (PPI) network analysis for the differential genes. MATERIALS AND METHODS: The CAD and ICM datasets were collected from the Gene Expression Omnibus (GEO) database for human tumors to extract data components of peripheral blood RNA of patients and normal people in GSE71226 and GSE9128 chips; "limma" package of "R" software was used to screen the differential genes, and "pheatmap" package was applied to construct heat maps for the differential genes; Cytoscape, Database for Annotation, Visualization and Integration Discovery (DAVID) and String platforms were utilized for PPI network analysis, Genome Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis on the selected differential genes. RESULTS: A total of 575 differential genes were screened from GSE71226, including 350 genes with up-regulated expression and 225 with down-regulated expression, which was statistically significant (p<0.05, fold change >1). 75 differential genes were screened from GSE9128, including 47 genes with up-regulated expression and 28 with down-regulated expression. By virtue of String, DAVID and Cytoscape software, the PPI network diagram was constructed, and GO and KEGG analyses were performed successfully. CONCLUSIONS: A total of 8 common differential genes are screened, and functional annotation and pathway analysis are conducted, which is conducive to further studying the interactions between the differentially expressed genes.
OBJECTIVE: This paper aims at screening the common differential genes of coronary atherosclerotic heart disease (CAD) and ischemic cardiomyopathy (ICM), and to conduct pathway analysis and protein-protein interaction (PPI) network analysis for the differential genes. MATERIALS AND METHODS: The CAD and ICM datasets were collected from the Gene Expression Omnibus (GEO) database for humantumors to extract data components of peripheral blood RNA of patients and normal people in GSE71226 and GSE9128 chips; "limma" package of "R" software was used to screen the differential genes, and "pheatmap" package was applied to construct heat maps for the differential genes; Cytoscape, Database for Annotation, Visualization and Integration Discovery (DAVID) and String platforms were utilized for PPI network analysis, Genome Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis on the selected differential genes. RESULTS: A total of 575 differential genes were screened from GSE71226, including 350 genes with up-regulated expression and 225 with down-regulated expression, which was statistically significant (p<0.05, fold change >1). 75 differential genes were screened from GSE9128, including 47 genes with up-regulated expression and 28 with down-regulated expression. By virtue of String, DAVID and Cytoscape software, the PPI network diagram was constructed, and GO and KEGG analyses were performed successfully. CONCLUSIONS: A total of 8 common differential genes are screened, and functional annotation and pathway analysis are conducted, which is conducive to further studying the interactions between the differentially expressed genes.
Authors: Wei Rao; Shan Wang; Marcin Duleba; Suchan Niroula; Kristina Goller; Jingzhong Xie; Rajasekaran Mahalingam; Rahul Neupane; Audrey-Ann Liew; Matthew Vincent; Kenichi Okuda; Wanda K O'Neal; Richard C Boucher; Burton F Dickey; Michael E Wechsler; Omar Ibrahim; John F Engelhardt; Tinne C J Mertens; Wei Wang; Soma S K Jyothula; Christopher P Crum; Harry Karmouty-Quintana; Kalpaj R Parekh; Mark L Metersky; Frank D McKeon; Wa Xian Journal: Cell Date: 2020-04-15 Impact factor: 41.582