Network-Based Inference of Hub Genes In Epithelial Membrane Protein 2-Treated Human RPE cells

Abstract

Backgrounds Identification of hub genes (HGs) using transcriptome data of human retinal pigment epithelial cells (hRPECs) samples treated with epithelial membrane protein 2 (EMP2) was helpful to accurately evaluate the functional relevance of genetic alterations in activity proteins (APs) in these cells. Results We performed differential expression genes (DEGs) analyses of public RNA-seq transcriptome data of EMP2 treated hRPECs, vector control (VC) and wild type (WT) hRPECs. VIPER (Virtual Inference of Protein activity by Enriched Regulon analysis) was used to convert DEGs outcomes to APs signatures and ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks) was used to construct transcription regulatory networks (TRNs) to identify hub genes (HGs). Conclusions In addition to identifying a significant fraction of DEGs among EMP2-OE groups and EMP-KD groups when compared to VC or WT groups, respectively, we also accurately inferred aberrant TGNs and found several HGs induced by EMP2-overexpressed hRPECs under hypoxia. Thus, we raised a hypothesis that EMP2 may regulate hRPECs angiogenesis via a PDGFA regulatory network, which would help to understand the complex biology of angiogenesis in EMP2 and hypoxia treated hRPECs.