Identification of hub genes and pathways associated with abdominal subcutaneous fat deposition in pig using a comprehensive bioinformatics strategy

Abstract

Abstract Background Abdominal subcutaneous fat deposition (ASFD) is not only related to meat quality in pig industry, but also to human health in medicine. It is of great value to elucidate the potential molecular mechanisms of ASFD. However, the molecular mechanisms of ASFD are still unclear. The present study aims to identify hub genes and key pathways correlated with ASFD using porcine mature adipocytes (MAs). Results Totals of 565 differentially expressed genes (DEGs) were identified between three obese and three lean pigs, and these DEGs were mainly involved in p53 signaling pathway, MAPK signaling pathway and fatty acid metabolism. A protein-protein interaction (PPI) network including 540 nodes and 1065 edges was constructed, and top ten genes with the highest degree scores were identified as hub genes (ABL1, HDAC1, CDC42, HDAC2, MRPS5, MRPS10, MDM2, JUP, RPL7L1, and UQCRFS1) in the whole PPI network. A miRNA-hub gene network including 563 miRNAs and ten hub genes was established, and three genes with more links including MDM2, HDAC2 and CDC42 were identified as key genes in miRNA-gene regulatory network. Conclusions The present study identified some hub genes and key pathways associated with ASFD by a comprehensive analysis, which provided some novel insights into the molecular mechanism involved in ASFD.