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Prediction of pivotal pathways and hub genes associated with osteoporosis by Gibbs sampling

  • Authors:
    • Yiyun Tan
    • Lei Liu
  • View Affiliations / Copyright

    Affiliations: Department of Spinal Surgery, Changsha Hospital of Traditional Chinese Medicine (Changsha Eighth Hospital), Changsha, Hunan 410000, P.R. China, Department of Pain, Qianfo Shan Hospital, Jinan, Shandong 250014, P.R. China
    Copyright: © Tan et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 2107-2112
    |
    Published online on: January 16, 2019
       https://doi.org/10.3892/etm.2019.7180
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Abstract

Osteoporosis (OP) is a common metabolic bone disease with high incidence, and is recognized as a major public health problem worldwide. It is essential to clarify the pathogenesis of the disease for improving the diagnosis, prevention and treatment of OP. The aim of this study was to clarify the pivotal pathways and hub genes in OP using Gibbs sampling. The gene expression profile datasets were obtained from Gene Expression Omnibus (GEO) database. The pathways were enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) with genes intersection ≥5 based on gene expression profile data. Then, the acquired pathways were converted into Markov chains (MC). Gibbs sampling was conducted to obtain a new MC. In addition, the average probabilities of each pathway in two states containing human mesenchymal stem cells (hMSC) _middle-aged and hMSC_elderly were calculated through Markov chain Monte Carlo (MCMC) algorithm. Moreover, gene expression variation was taken into account to adjust the probability. Pivotal pathways were identified under adjusted posterior value >0.8. Then, Gibbs sampling was implemented to find hub genes from pathways. There were 280 pathways determined by the gene intersection ≥5. Gibbs sampling identified two disturbed pathways (pathways in cancer and influenza A) and two hub genes (cyclin A1 and WNT2) under the adjusted probability >0.8. Gene expression analysis showed that all the disturbed pathways and hub genes had increased expression levels in hMSC_middle-aged samples compared with hMSC_elderly samples. We identified two pivotal pathways and two hub genes in OP using Gibbs sampling. The results contribute to the understanding of underlying pathogenesis and could be considered as potential biomarkers for the therapy of OP.
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1 

Muschitz C, Kocijan R, Haschka J, Pahr D, Kaider A, Pietschmann P, Hans D, Muschitz GK, Fahrleitner-Pammer A and Resch H: TBS reflects trabecular microarchitecture in premenopausal women and men with idiopathic osteoporosis and low-traumatic fractures. Bone. 79:259–266. 2015. View Article : Google Scholar : PubMed/NCBI

2 

Harsløf T and Langdahl BL: New horizons in osteoporosis therapies. Curr Opin Pharmacol. 28:38–42. 2016. View Article : Google Scholar : PubMed/NCBI

3 

Wright NC, Looker AC, Saag KG, Curtis JR, Delzell ES, Randall S and Dawson-Hughes B: The recent prevalence of osteoporosis and low bone mass in the United States based on bone mineral density at the femoral neck or lumbar spine. J Bone Miner Res. 29:2520–2526. 2014. View Article : Google Scholar : PubMed/NCBI

4 

Zhang D, Ge Z, Ma X, Zhi L, Zhang Y, Wu X, Yao S and Ma W: Genetic association study identified a 20 kb regulatory element in WLS associated with osteoporosis and bone mineral density in Han Chinese. Sci Rep. 7:136682017. View Article : Google Scholar : PubMed/NCBI

5 

Mohammadi Z, Fayyazbakhsh F, Ebrahimi M, Amoli MM, Khashayar P, Dini M, Zadeh RN, Keshtkar A and Barikani HR: Association between vitamin D receptor gene polymorphisms (Fok1 and Bsm1) and osteoporosis: A systematic review. J Diabetes Metab Disord. 13:982014. View Article : Google Scholar : PubMed/NCBI

6 

Xiao P, Chen Y, Jiang H, Liu YZ, Pan F, Yang TL, Tang ZH, Larsen JA, Lappe JM, Recker RR, et al: In vivo genome-wide expression study on human circulating B cells suggests a novel ESR1 and MAPK3 network for postmenopausal osteoporosis. J Bone Miner Res. 23:644–654. 2008. View Article : Google Scholar : PubMed/NCBI

7 

Astiazarán MC, Cervantes-Sodi M, Rebolledo-Enríquez E, Chacón-Camacho O, Villegas V and Zenteno JC: Novel homozygous LRP5 mutations in Mexican patients with osteoporosis-pseudoglioma syndrome. Genet Test Mol Biomarkers. 21:742–746. 2017. View Article : Google Scholar : PubMed/NCBI

8 

Li JJ, Wang BQ, Fei Q, Yang Y and Li D: Identification of candidate genes in osteoporosis by integrated microarray analysis. Bone Joint Res. 5:594–601. 2016. View Article : Google Scholar : PubMed/NCBI

9 

Xie W, Ji L, Zhao T and Gao P: Identification of transcriptional factors and key genes in primary osteoporosis by DNA microarray. Med Sci Monit. 21:1333–1344. 2015. View Article : Google Scholar : PubMed/NCBI

10 

Pei C, Wang SL, Fang J and Zhang W: GSMC: Combining parallel Gibbs sampling with maximal cliques for hunting DNA motif. J Comput Biol. 24:1243–1253. 2017. View Article : Google Scholar : PubMed/NCBI

11 

Nan N, Chen Q, Wang Y, Zhai X, Yang CC, Cao B and Chong T: Screening disrupted molecular functions and pathways associated with clear cell renal cell carcinoma using Gibbs sampling. Comput Biol Chem. 70:15–20. 2017. View Article : Google Scholar : PubMed/NCBI

12 

Chen P, Guo LH, Guo YK, Qu ZJ, Gao Y and Qiu H: Identification of disturbed pathways in heart failure based on Gibbs sampling and pathway enrichment analysis. Genet Mol Res. 15:gmr79562016.

13 

Yang K, Wang X, Zhang H, Wang Z, Nan G, Li Y, Zhang F, Mohammed MK, Haydon RC, Luu HH, et al: The evolving roles of canonical WNT signaling in stem cells and tumorigenesis: Implications in targeted cancer therapies. Lab Invest. 96:116–136. 2016. View Article : Google Scholar : PubMed/NCBI

14 

Park JI: Growth arrest signaling of the Raf/MEK/ERK pathway in cancer. Front Biol (Beijing). 9:95–103. 2014. View Article : Google Scholar : PubMed/NCBI

15 

Gasparri ML, Bardhi E, Ruscito I, Papadia A, Farooqi AA, Marchetti C, Bogani G, Ceccacci I, Mueller MD and Benedetti Panici P: PI3K/AKT/mTOR pathway in ovarian cancer treatment: Are we on the right track? Geburtshilfe Frauenheilkd. 77:1095–1103. 2017. View Article : Google Scholar : PubMed/NCBI

16 

Luo G, Xu B and Huang Y: Icariside II promotes the osteogenic differentiation of canine bone marrow mesenchymal stem cells via the PI3K/AKT/mTOR/S6K1 signaling pathways. Am J Transl Res. 9:2077–2087. 2017.PubMed/NCBI

17 

Zhang JH, Xin J, Fan LX and Yin H: Intervention effects of Zuoguiwan containing serum on osteoblast through ERK1/2 and Wnt/β-catenin signaling pathway in models with kidney-Yang-deficiency, kidney-Yin-deficiency osteoporosis syndromes. Zhongguo Zhong Yao Za Zhi. 42:3983–3989. 2017.(In Chinese). PubMed/NCBI

18 

Marjuki H, Gornitzky A, Marathe BM, Ilyushina NA, Aldridge JR, Desai G, Webby RJ and Webster RG: Influenza A virus-induced early activation of ERK and PI3K mediates V-ATPase-dependent intracellular pH change required for fusion. Cell Microbiol. 13:587–601. 2011. View Article : Google Scholar : PubMed/NCBI

19 

Dam S, Kracht M, Pleschka S and Schmitz ML: The influenza A virus genotype determines the antiviral function of NF-κB. J Virol. 90:7980–7990. 2016. View Article : Google Scholar : PubMed/NCBI

20 

Zhou RP, Lin SJ, Wan WB, Zuo HL, Yao FF, Ruan HB, Xu J, Song W, Zhou YC, Wen SY, et al: Chlorogenic acid prevents osteoporosis by Shp2/PI3K/Akt pathway in ovariectomized rats. PLoS One. 11:e01667512016. View Article : Google Scholar : PubMed/NCBI

21 

Wang X, Chen L and Peng W: Protective effects of resveratrol on osteoporosis via activation of the SIRT1-NF-κB signaling pathway in rats. Exp Ther Med. 14:5032–5038. 2017.PubMed/NCBI

22 

Yang B, Miao S, Zhang LN, Sun HB, Xu ZN and Han CS: Correlation of CCNA1 promoter methylation with malignant tumors: A meta-analysis introduction. Biomed Res Int. 2015:1340272015.PubMed/NCBI

23 

Miftakhova R, Hedblom A, Batkiewicz L, Anagnosaki L, Zhang Y, Sjölander A, Wingren AG, Wolgemuth DJ and Persson JL: Cyclin A1 regulates the interactions between mouse haematopoietic stem and progenitor cells and their niches. Cell Cycle. 14:1948–1960. 2015. View Article : Google Scholar : PubMed/NCBI

24 

Yu S, Sharma R, Nie D, Jiao H, Im HJ, Lai Y, Zhao Z, Zhu K, Fan J, Chen D, et al: ADAR1 ablation decreases bone mass by impairing osteoblast function in mice. Gene. 513:101–110. 2013. View Article : Google Scholar : PubMed/NCBI

25 

Huang C, Ma R, Xu Y, Li N, Li Z, Yue J, Li H, Guo Y and Qi D: Wnt2 promotes non-small cell lung cancer progression by activating WNT/β-catenin pathway. Am J Cancer Res. 5:1032–1046. 2015.PubMed/NCBI

26 

Jiang H, Li Q, He C, Li F, Sheng H, Shen X, Zhang X, Zhu S, Chen H, Chen X, et al: Activation of the Wnt pathway through Wnt2 promotes metastasis in pancreatic cancer. Am J Cancer Res. 4:537–544. 2014.PubMed/NCBI

27 

Tan SH, Senarath-Yapa K, Chung MT, Longaker MT, Wu JY and Nusse R: Wnts produced by Osterix-expressing osteolineage cells regulate their proliferation and differentiation. Proc Natl Acad Sci USA. 111:E5262–E5271. 2014. View Article : Google Scholar : PubMed/NCBI

28 

Monroe DG, McGee-Lawrence ME, Oursler MJ and Westendorf JJ: Update on Wnt signaling in bone cell biology and bone disease. Gene. 492:1–18. 2012. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Tan Y and Liu L: Prediction of pivotal pathways and hub genes associated with osteoporosis by Gibbs sampling. Exp Ther Med 17: 2107-2112, 2019.
APA
Tan, Y., & Liu, L. (2019). Prediction of pivotal pathways and hub genes associated with osteoporosis by Gibbs sampling. Experimental and Therapeutic Medicine, 17, 2107-2112. https://doi.org/10.3892/etm.2019.7180
MLA
Tan, Y., Liu, L."Prediction of pivotal pathways and hub genes associated with osteoporosis by Gibbs sampling". Experimental and Therapeutic Medicine 17.3 (2019): 2107-2112.
Chicago
Tan, Y., Liu, L."Prediction of pivotal pathways and hub genes associated with osteoporosis by Gibbs sampling". Experimental and Therapeutic Medicine 17, no. 3 (2019): 2107-2112. https://doi.org/10.3892/etm.2019.7180
Copy and paste a formatted citation
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Spandidos Publications style
Tan Y and Liu L: Prediction of pivotal pathways and hub genes associated with osteoporosis by Gibbs sampling. Exp Ther Med 17: 2107-2112, 2019.
APA
Tan, Y., & Liu, L. (2019). Prediction of pivotal pathways and hub genes associated with osteoporosis by Gibbs sampling. Experimental and Therapeutic Medicine, 17, 2107-2112. https://doi.org/10.3892/etm.2019.7180
MLA
Tan, Y., Liu, L."Prediction of pivotal pathways and hub genes associated with osteoporosis by Gibbs sampling". Experimental and Therapeutic Medicine 17.3 (2019): 2107-2112.
Chicago
Tan, Y., Liu, L."Prediction of pivotal pathways and hub genes associated with osteoporosis by Gibbs sampling". Experimental and Therapeutic Medicine 17, no. 3 (2019): 2107-2112. https://doi.org/10.3892/etm.2019.7180
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