Bioinformatics analysis of differentially expressed genes in endometrium with recurrent implantation failure

Abstract

Objective To investigate the related genes in the endometrium with recurrent implantation failure (RIF) after in vitro fertilization (IVF) by bioinformatics analysis in order to illustrate the underlying pathogenesis of RIF. Methods The dataset GSE111974 was downloaded from Gene Expression Omnibus (GEO) in National Center for Biotechnology Information (NCBI). R/Bioconductor packages "marray" and "limma" were applied to this model to screen out the differentially expressed gene (DEGs) in the patients with RIF compared with normal fertile controls. Then, the database for annotation, visualization and integrated discovery (DAVID) was employed to make Gene Ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis to analyze the protein-protein interaction network by the Search Tool for the Retrieval of Interacting Genes (STRING) online database and Cytoscape software. Results There were 170 DEGs turning out, of which 127 genes were up-regulated and 43 were down-regulated. GO analysis shows that the DEGs mainly concentrate in cell membrane, endoplasmic reticulum and other areas, which primarily participate in oxidation-reduction process, cell cycle arrest and lipid metabolic process, etc. Their molecular functions are involved in heme binding, signal transducer activity, retinoic acid binding and peroxidase activity. KEGG pathway analysis showed that these genes are mainly involved in metabolic pathways, oxytocin signaling pathway, and TNF signaling pathway, etc. STRING online database and Cytoscape software found out that DEGs PTGS2, TOP2A and ACTA2 were the hub genes of RIF. Conclusion The key genes PTGS2, TOP2A and ACTA2 and transcription factors CEBPB, CDX2 and ESR1 may play important role in the pathogenesis of RIF.

Keywords

• recurrent implantation failure
• endometrium
• bioinformatics
• gene