Investigation of gene expression and genetic simultaneous control associated with erectile dysfunction and diabetes

Diabetes can cause some diseases or abnormalities. One of the disorders caused by diabetes may be erectile dysfunction (ED). ED is sexual dysfunction characterized by the inability to establish or maintain an erect penis during sexual activity and is a common problem of men with chronic type 2 diabetes. These processes, disorders and diseases are highly influenced by the genetics of individuals. In this study, the relationship between genes and diabetes and ED has been explored by a system biology approach. For this purpose, the samples from ten control and diabetic-ED rats were collected. After a search in Gene Expression Omnibus (GEO), series with accession number GSE2457 comprising of 5 normal and 5 diabetic-ED rats were selected. Raw CEL files of these samples were normalized with robust multi-array average (RMA) expression measure method by using the linear models for microarray data (LIMMA) R package. The extracted probe IDs were transformed into 10451 unique and validated official gene symbols. Then, differentially expressed genes (DEGs) were identified between control and normal penile mucosa by employing the LIMMA R package. DEGs were classified by utilizing KEGG to underlying pathways by Enrichr. The expression values of DEGs were used to construct a gene regulatory network (GRN), by the GENEI3 R package. To analyze the topology of constructed GRNs, betweenness centrality was calculated. Genes with higher betweenness centrality scores were then identified, through the CytoNCA. We then took the commonality of DEGs genes and high-top ranking genes from CytoNCA via a predicted interaction network using GeneMANIA as the most likely important genes in erectile dysfunction. Among the 374 DEGs studied, 146 DEGs showed up-regulation and 228 DEGs displayed down-regulation expression in diabetic-ED rats. According to the Volcano plot, the dpp4, LOC102553868, Ndufa412, Oxct1, Atp2b3 and Zfp91 gene down-regulated and Lpl, Retsat, B4galt1 and Pdk4 genes up-regulated in ED and diabetic rats. Furthermore, genes like dpp4 acted as hubs in the inferred GRN.