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

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 pa...

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Autores principales: Zhang, Ya-Peng, Ao, Shuang, Liu, Yu, Wang, Yu, Jia, Yi-Ming, Zhang, Hao, Leng, Hui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: D.A. Spandidos 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425251/
https://www.ncbi.nlm.nih.gov/pubmed/30906457
http://dx.doi.org/10.3892/etm.2019.7231
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author Zhang, Ya-Peng
Ao, Shuang
Liu, Yu
Wang, Yu
Jia, Yi-Ming
Zhang, Hao
Leng, Hui
author_facet Zhang, Ya-Peng
Ao, Shuang
Liu, Yu
Wang, Yu
Jia, Yi-Ming
Zhang, Hao
Leng, Hui
author_sort Zhang, Ya-Peng
collection PubMed
description 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.
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spelling pubmed-64252512019-03-22 Identification of hub genes associated with postmenopausal osteoporosis by Gibbs sampling method Zhang, Ya-Peng Ao, Shuang Liu, Yu Wang, Yu Jia, Yi-Ming Zhang, Hao Leng, Hui Exp Ther Med Articles 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. D.A. Spandidos 2019-04 2019-02-01 /pmc/articles/PMC6425251/ /pubmed/30906457 http://dx.doi.org/10.3892/etm.2019.7231 Text en Copyright: © Zhang et al. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
spellingShingle Articles
Zhang, Ya-Peng
Ao, Shuang
Liu, Yu
Wang, Yu
Jia, Yi-Ming
Zhang, Hao
Leng, Hui
Identification of hub genes associated with postmenopausal osteoporosis by Gibbs sampling method
title Identification of hub genes associated with postmenopausal osteoporosis by Gibbs sampling method
title_full Identification of hub genes associated with postmenopausal osteoporosis by Gibbs sampling method
title_fullStr Identification of hub genes associated with postmenopausal osteoporosis by Gibbs sampling method
title_full_unstemmed Identification of hub genes associated with postmenopausal osteoporosis by Gibbs sampling method
title_short Identification of hub genes associated with postmenopausal osteoporosis by Gibbs sampling method
title_sort identification of hub genes associated with postmenopausal osteoporosis by gibbs sampling method
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425251/
https://www.ncbi.nlm.nih.gov/pubmed/30906457
http://dx.doi.org/10.3892/etm.2019.7231
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