Integrated analysis of hub genes and miRNA- transcription factor-hub gene interaction network in necrotizing enterocolitis

Abstract

Background The aim of this study was to identify hub genes, related transcription factors (TFs) and miRNAs from the miRNA–TF–gene interaction network in necrotizing enterocolitis (NEC). Methods Three expression data sets from GEO database that compared NEC with surgical negative controls were used to calculate differentially expressed miRNAs (DEMis) and genes (DEGs). A protein-protein interaction (PPI) network was constructed using DEGs and was used to determine hub genes. miRNAs related to hub genes were identified from the intersection between DEMis and predictions of hub gene-miRNA pairs using Starbase, TFs were predicted by hub genes, TF-miRNA pairs were predicted using miRNet. Finally, the miRNA–TF–hub gene interaction network was formed using these predicted pairs. Results A total of 14 DEMis and 123 DEGs were identified from the GEO datasets. One hundred and twenty DEGs were found in the PPI network. A pathogenic-associated interaction network was created by intersecting miRNAs, predicted TFs and hub genes. Article-published RNAs such as hsa-miR-7 or TLR4 were shown in this network, and novel RNAs and TFs (Hsa-miR-200a, GATA3, CXCL5) were shown in the network as important regulator. Conclusions This analysis displayed several important hub genes, TFs and miRNAs, some of which were not fully understood in previous studies of NEC. These results may play an important role in future studies on the etiology or treatment of NEC.