Identification of hub genes associated with postmenopausal osteoporosis by Gibbs sampling method.

Abstract

Underlying pivotal pathways were identified to reveal potential key genes correlated with postmenopausal osteoporosis (PMOP). The pathways were enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) with genes intersection greater than 5 based on gene expression profile data, and the acquired pathways were then transformed to Markov chain (MC). Gibbs sampling was conducted to obtain a new MC. Moreover, the average probabilities of each pathway in normal and PMOP were computed via an MC Monte Carlo (MCMC) algorithm, and differential pathways were identified based on probabilities more than 0.7. In addition, frequencies of appearance of pathway genes were counted via MCMC and the hub genes were achieved with the probabilities of gene expression efficiencies in two states. Judging by the gene intersection more than 5, overall 280 pathways were determined. After Gibbs sampling, 2 differential pathways were obtained on the basis of probabilities more than 0.7. Moreover, the hub genes comprising TNNC1, MYL2, and TTN were achieved according to probabilities more than 0.7. The identified pathways and the three hub genes probably are useful for developing approaches for the diagnosis and treatment of PMOP in future preclinical and clinical applications.