Open Access

Hub genes and gene functions associated with postmenopausal osteoporosis predicted by an integrated method

  • Authors:
    • Honghai Cao
    • Lihai Zhang
    • Hua Chen
    • Wei Zhang
    • Qun Zhang
    • Xiangdang Liang
    • Yizhu Guo
    • Peifu Tang
  • View Affiliations

  • Published online on: December 13, 2018     https://doi.org/10.3892/etm.2018.7095
  • Pages: 1262-1267
  • Copyright: © Cao et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Postmenopausal osteoporosis (PO) imposes great burden on individuals and society. This study predicted hub genes and gene functions for PO by an integration of the convergent evidence (CE) method, rank product (RP) algorithm and the combing of P-values. Using the gene expression data, genes were ranked by the CE method, RP algorithm and combing P-values, respectively. Subsequently, the top 100 genes were selected from each of the three gene lists, and then the common genes for two or three methods were denoted as informative genes of PO. A mutual information network (MIN) was constructed for the informative genes utilizing the context likelihood of relatedness algorithm. Topological centrality (degree) analysis was conducted on the MIN to investigate hub genes. Then we performed Gene Ontology (GO) enrichment analysis dependent upon the Biological Networks Gene Ontology tool (BiNGO) plugin of Cytoscape to investigate hub gene functions for PO patients. Consequently, a total of 82 informative genes were obtained by integrating the results of the three methods. There were 82 nodes and 1,741 edges in the MIN, of which 8 hub genes were identified, such as PFN1, EEF2 and S100A9. The result of GO enrichment analysis showed that 49 GO terms with P<0.001 were detected, especially the top 5 gene sets were defined as hub gene functions of PO, for instance, translational elongation, translation and cellular macromolecule biosynthetic process. In conclusion, we have predicted 8 hub genes and 5 hub gene functions associated with PO patients. The findings might help understand the molecular mechanism underlying PO.
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February-2019
Volume 17 Issue 2

Print ISSN: 1792-0981
Online ISSN:1792-1015

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Spandidos Publications style
Cao H, Zhang L, Chen H, Zhang W, Zhang Q, Liang X, Guo Y and Tang P: Hub genes and gene functions associated with postmenopausal osteoporosis predicted by an integrated method. Exp Ther Med 17: 1262-1267, 2019
APA
Cao, H., Zhang, L., Chen, H., Zhang, W., Zhang, Q., Liang, X. ... Tang, P. (2019). Hub genes and gene functions associated with postmenopausal osteoporosis predicted by an integrated method. Experimental and Therapeutic Medicine, 17, 1262-1267. https://doi.org/10.3892/etm.2018.7095
MLA
Cao, H., Zhang, L., Chen, H., Zhang, W., Zhang, Q., Liang, X., Guo, Y., Tang, P."Hub genes and gene functions associated with postmenopausal osteoporosis predicted by an integrated method". Experimental and Therapeutic Medicine 17.2 (2019): 1262-1267.
Chicago
Cao, H., Zhang, L., Chen, H., Zhang, W., Zhang, Q., Liang, X., Guo, Y., Tang, P."Hub genes and gene functions associated with postmenopausal osteoporosis predicted by an integrated method". Experimental and Therapeutic Medicine 17, no. 2 (2019): 1262-1267. https://doi.org/10.3892/etm.2018.7095