Open Access

Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome

  • Authors:
    • Haoran Shen
    • Zhou Liang
    • Saihua Zheng
    • Xuelian Li
  • View Affiliations

  • Published online on: September 20, 2017     https://doi.org/10.3892/ijmm.2017.3146
  • Pages: 1385-1396
  • Copyright: © Shen et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

The purpose of this study was to identify promising candidate genes and pathways in polycystic ovary syndrome (PCOS). Microarray dataset GSE345269 obtained from the Gene Expression Omnibus database includes 7 granulosa cell samples from PCOS patients, and 3 normal granulosa cell samples. Differentially expressed genes (DEGs) were screened between PCOS and normal samples. Pathway enrichment analysis was conducted for DEGs using ClueGO and CluePedia plugin of Cytoscape. A Reactome functional interaction (FI) network of the DEGs was built using ReactomeFIViz, and then network modules were extracted, followed by pathway enrichment analysis for the modules. Expression of DEGs in granulosa cell samples was measured using quantitative RT-PCR. A total of 674 DEGs were retained, which were significantly enriched with inflammation and immune-related pathways. Eight modules were extracted from the Reactome FI network. Pathway enrichment analysis revealed significant pathways of each module: module 0, Regulation of RhoA activity and Signaling by Rho GTPases pathways shared ARHGAP4 and ARHGAP9; module 2, GlycoProtein VI-mediated activation cascade pathway was enriched with RHOG; module 3, Thromboxane A2 receptor signaling, Chemokine signaling pathway, CXCR4-mediated signaling events pathways were enriched with LYN, the hub gene of module 3. Results of RT-PCR confirmed the finding of the bioinformatic analysis that ARHGAP4, ARHGAP9, RHOG and LYN were significantly upregulated in PCOS. RhoA-related pathways, GlycoProtein VI-mediated activation cascade pathway, ARHGAP4, ARHGAP9, RHOG and LYN may be involved in the pathogenesis of PCOS.
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November-2017
Volume 40 Issue 5

Print ISSN: 1107-3756
Online ISSN:1791-244X

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Spandidos Publications style
Shen H, Liang Z, Zheng S and Li X: Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome. Int J Mol Med 40: 1385-1396, 2017
APA
Shen, H., Liang, Z., Zheng, S., & Li, X. (2017). Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome. International Journal of Molecular Medicine, 40, 1385-1396. https://doi.org/10.3892/ijmm.2017.3146
MLA
Shen, H., Liang, Z., Zheng, S., Li, X."Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome". International Journal of Molecular Medicine 40.5 (2017): 1385-1396.
Chicago
Shen, H., Liang, Z., Zheng, S., Li, X."Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome". International Journal of Molecular Medicine 40, no. 5 (2017): 1385-1396. https://doi.org/10.3892/ijmm.2017.3146