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Start Over Author "Weiyuan Ye" Publisher public library of science (plos)
2 results on '"Weiyuan Ye"'

1. Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome-Wide Association Studies.

Author

Longjuan Qin, Yuyong Liu, Ya Wang, Guiju Wu, Jie Chen, Weiyuan Ye, Jiancai Yang, and Qingyang Huang

Subjects
Medicine, Science
Abstract

OBJECTIVES:Genome-wide association studies (GWASs) have revealed many SNPs and genes associated with osteoporosis. However, influence of these SNPs and genes on the predisposition to osteoporosis is not fully understood. We aimed to identify osteoporosis GWASs-associated SNPs potentially influencing the binding affinity of transcription factors and miRNAs, and reveal enrichment signaling pathway and "hub" genes of osteoporosis GWAS-associated genes. METHODS:We conducted multiple computational analyses to explore function and mechanisms of osteoporosis GWAS-associated SNPs and genes, including SNP conservation analysis and functional annotation (influence of SNPs on transcription factors and miRNA binding), gene ontology analysis, pathway analysis and protein-protein interaction analysis. RESULTS:Our results suggested that a number of SNPs potentially influence the binding affinity of transcription factors (NFATC2, MEF2C, SOX9, RUNX2, ESR2, FOXA1 and STAT3) and miRNAs. Osteoporosis GWASs-associated genes showed enrichment of Wnt signaling pathway, basal cell carcinoma and Hedgehog signaling pathway. Highly interconnected "hub" genes revealed by interaction network analysis are RUNX2, SP7, TNFRSF11B, LRP5, DKK1, ESR1 and SOST. CONCLUSIONS:Our results provided the targets for further experimental assessment and further insight on osteoporosis pathophysiology.

Published
2016
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2. Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome-Wide Association Studies

Author

Jie Chen, Ya Wang, Longjuan Qin, Jiancai Yang, Qingyang Huang, Guiju Wu, Yuyong Liu, and Weiyuan Ye

Subjects
0301 basic medicine, lcsh:Medicine, Genome-wide association study, Biochemistry, Binding Analysis, Database and Informatics Methods, 0302 clinical medicine, Polymorphism (computer science), Genotype, Medicine and Health Sciences, Connective Tissue Diseases, lcsh:Science, Genetics, Multidisciplinary, Gene Ontologies, Genomics, Genomic Databases, Nucleic acids, Research Article, Single-nucleotide polymorphism, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, 03 medical and health sciences, Rheumatology, Gene Types, microRNA, Genome-Wide Association Studies, Humans, Genetic Predisposition to Disease, Non-coding RNA, Transcription factor, Gene, Chemical Characterization, Genetic association, Biology and life sciences, lcsh:R, Computational Biology, Human Genetics, Genome Analysis, Gene regulation, MicroRNAs, Biological Databases, 030104 developmental biology, Osteoporosis, RNA, Regulator Genes, lcsh:Q, Gene expression, 030217 neurology & neurosurgery, Genome-Wide Association Study, Transcription Factors
Abstract

Objectives Genome-wide association studies (GWASs) have revealed many SNPs and genes associated with osteoporosis. However, influence of these SNPs and genes on the predisposition to osteoporosis is not fully understood. We aimed to identify osteoporosis GWASs-associated SNPs potentially influencing the binding affinity of transcription factors and miRNAs, and reveal enrichment signaling pathway and “hub” genes of osteoporosis GWAS-associated genes. Methods We conducted multiple computational analyses to explore function and mechanisms of osteoporosis GWAS-associated SNPs and genes, including SNP conservation analysis and functional annotation (influence of SNPs on transcription factors and miRNA binding), gene ontology analysis, pathway analysis and protein-protein interaction analysis. Results Our results suggested that a number of SNPs potentially influence the binding affinity of transcription factors (NFATC2, MEF2C, SOX9, RUNX2, ESR2, FOXA1 and STAT3) and miRNAs. Osteoporosis GWASs-associated genes showed enrichment of Wnt signaling pathway, basal cell carcinoma and Hedgehog signaling pathway. Highly interconnected “hub” genes revealed by interaction network analysis are RUNX2, SP7, TNFRSF11B, LRP5, DKK1, ESR1 and SOST. Conclusions Our results provided the targets for further experimental assessment and further insight on osteoporosis pathophysiology.

Published
2016

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