Identification of new progestogen-associated networks in mammalian ovulation using bioinformatics

Abstract

BackgroundProgesterone plays an essential role in mammalian ovulation. Although much is known about this process, the gene networks involved in ovulation have yet to be established. When analyze the mechanisms of ovulation, we often need to determine key genes or pathways to investigate the reproduction features. However, traditional experimental methods have a number of limitations.ResultsData, in this study, were acquired from GSE41836 and GSE54584 which provided different samples. They were analyzed with the GEO2R and 546 differentially expressed genes were obtained from two data sets using bioinformatics (absolute log2 FC > 1, P < 0.05). This study identified four genes (PGR, RELN, PDE10A and PLA2G4A) by protein-protein interaction networks and pathway analysis, and their functional enrichments were associated with ovulation. Then, the top 25 statistical pathway enrichments related to hCG treatment were analyzed. Furthermore, gene network analysis identified certain interconnected genes and pathways involved in progestogenic mechanisms, including progesterone-mediated oocyte maturation, the MAPK signaling pathway, the GnRH signaling pathway and focal adhesion, etc. Moreover, we explored the four target gene pathways. q-PCR analysis following hCG and RU486 treatments confirmed the certain novel progestogenic-associated genes (GNAI1, PRKCA, CAV1, EGFR, RHOA, ZYX, VCL, GRB2 and RAP1A).ConclusionsThe results suggested four key genes, nine predicted genes and eight pathways to be involved in progestogenic networks. These networks provide important regulatory genes and signaling pathways which are involved in ovulation. This study provides a fundamental basis for subsequent functional studies to investigate the regulation of mammalian ovulation.Electronic supplementary materialThe online version of this article (10.1186/s12918-018-0577-7) contains supplementary material, which is available to authorized users.

Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep

“…In another study ovarian proteome of hyper-prolificacy sheep was analyzed and more than 100 identified proteins were classified in carbohydrate transport and metabolism [ 76 ]. Also, Yang et al [ 77 ] using transcriptome analysis, reported galactose metabolism and fructose and mannose metabolism as biological pathways affecting ovulation. Many GO terms related to cell communication such as biological adhesion (GO:0022610), cell adhesion (GO:0007155), cell junction (GO:0030054), and cell-cell adherens junction (GO:0005913) were identified.…”

“…cGMP) to support the oocyte development, metabolism, and hemostasis [ 79 ]. Many genomics, transcriptomics, and proteomics studies reported many pathways related to both cell adhesion and gap junction process as pathways which has vital roles in prolificacy [ 49 , 62 , 77 , 80 , 81 ].…”

Ovary-derived circular RNAs profile analysis during the onset of puberty in gilts

“…There is evidence that FAF1 , Fas-associated protein factor 1, is expressed in the cytoplasm of growing oocyte of the ovary [ 63 ]. Yang et al have provided that LRP8 is the progestogenic-associated gene [ 64 ]. These results suggest that the tissue-specific circRNAs might regulate the transcriptions of their parental genes to involve in the onset of puberty.…”

Phosphodiesterase 10A (PDE10A) as a novel target to suppress β-catenin and RAS signaling in epithelial ovarian cancer

“…Although PDEs and cyclic nucleotides play a critical role in the ovary, namely in regulating folliculogenesis, oocyte maturation, and ovulation, PDE10A has not been widely studied in this regard [28,29]. The most notable research on PDE10A and ovulation comes from a bioinformatics analysis of microarrays in hCG stimulated mouse preovulatory follicles, where PDE10A was reported to be one of four essential genes in progesterone-related ovulatory networks [30].…”