G Li1, X-J Wu, X-Q Kong, L Wang, X Jin. 1. Department of Vascular Surgery, Shandong Provincial Hospital Aaffiliated to Shandong University, Jinan, P.R. China. jinxingjxjx@hotmail.com.
Abstract
OBJECTIVE: The aim of the study is to explore the potential familial hypercholesterolemia markers by comparing with healthy controls. MATERIAL AND METHODS: We downloaded the gene expression profile GSE13985 from Gene Expression Omnibus database including five patients diagnosed with familial hypercholesterolemia (FH) and five age, sex, status matched controls. We applied t-test, Wilcox test and Fisher test in Multtest package of R language to identify the differentially expressed genes (DEGs) with p < 0.05 and |logFC| > 1, and constructed the interaction network of the top 3 up- and down-regulated genes using STRING. Besides, the modules of network were analyzed with Cytoscape and screened out with Mcode plugin, and the functional annotation of the genes involved in the modules was analyzed with BiNGO (Biological Networks Gene Ontology). RESULTS: Firstly, totally 101 differentially expressed genes were identified in FH samples compared with control samples, the genes ranked in top 3 up- and down-regulated genes were selected. Then, basing on the interaction network of these selected genes, ribosomal L24 domain containing 1 (RSL24D1) and cytochrome c oxidase subunit VIIb (COX7B) showed a central position in the interaction network, and also exited in the modules of the network. The functional annotation of the genes in modules showed that COX7B was associated with oxidative phosphorylation. CONCLUSIONS: COX7B might play vital roles in FH via oxidative phosphorylation system, and might be potential target in the treatment of FH.
OBJECTIVE: The aim of the study is to explore the potential familial hypercholesterolemia markers by comparing with healthy controls. MATERIAL AND METHODS: We downloaded the gene expression profile GSE13985 from Gene Expression Omnibus database including five patients diagnosed with familial hypercholesterolemia (FH) and five age, sex, status matched controls. We applied t-test, Wilcox test and Fisher test in Multtest package of R language to identify the differentially expressed genes (DEGs) with p < 0.05 and |logFC| > 1, and constructed the interaction network of the top 3 up- and down-regulated genes using STRING. Besides, the modules of network were analyzed with Cytoscape and screened out with Mcode plugin, and the functional annotation of the genes involved in the modules was analyzed with BiNGO (Biological Networks Gene Ontology). RESULTS: Firstly, totally 101 differentially expressed genes were identified in FH samples compared with control samples, the genes ranked in top 3 up- and down-regulated genes were selected. Then, basing on the interaction network of these selected genes, ribosomal L24 domain containing 1 (RSL24D1) and cytochrome c oxidase subunit VIIb (COX7B) showed a central position in the interaction network, and also exited in the modules of the network. The functional annotation of the genes in modules showed that COX7B was associated with oxidative phosphorylation. CONCLUSIONS:COX7B might play vital roles in FH via oxidative phosphorylation system, and might be potential target in the treatment of FH.