Searching for perturbed biological pathways and genes through analyzing the expression profile changes in osteoclasts after treatment by bisphosphonates

Criticality pathways and genes related to osteoporosis were identified. We downloaded the expression data of osteoclasts treated with or without bisphosphonates and all human pathways from the public database. Gibbs sampling and Markov chain were performed to identify the disturbed pathways and the hub genes in the disturbed pathways. Pathways and genes with adjusted probability (α(adj)) ≥0.75 were considered as the disturbed pathways and hub genes. We identified four disturbed pathways (Maturity onset diabetes of the young, Olfactory transduction, Cyanoamino acid metabolism, Taurine and hypotaurine metabolism) and two hub genes (OR2A4 and NKX2-2) with α(adj) ≥0.75. The expression levels of these disturbed pathways and hub genes were downregulated in bisphosphonates group. In conclusion, four disturbed pathways and two hub genes related to osteoporosis were identified. These results give us a better understanding of the potential mechanism of bisphosphonate treatment and the pathogenesis of osteoporosis.