| Literature DB >> 26930606 |
Longjuan Qin1, Yuyong Liu1, Ya Wang1, Guiju Wu1, Jie Chen1, Weiyuan Ye1, Jiancai Yang2, Qingyang Huang1.
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.Entities:
Mesh:
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Year: 2016 PMID: 26930606 PMCID: PMC4773152 DOI: 10.1371/journal.pone.0150070
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Fig 1The workflow of osteoporosis-associated loci identified by GWAS.
Conservation analysis of osteoporosis GWAS-associated lead SNPs.
| SNPs | VISTA | UCSC | |
|---|---|---|---|
| Mouse ( | Chimp ( | ||
| rs7741021 | 1.10E-03 | - | 6/9 |
| rs4355801 | 4.60E-03 | 0.1 | 5/9 |
| rs7071206 | - | 9.10E-08 | 5/9 |
| rs227425 | 8.20E-05 | - | 5/9 |
| rs9287237 | - | 1.80E-10 | 4/9 |
| rs2952559 | - | 6.90E-03 | 4/9 |
| rs3801387 | 7.30E-20 | 4.60E-03 | 4/9 |
| rs4233949 | 1.80E-03 | - | 4/9 |
| rs9533095 | - | 1.40E-02 | 4/9 |
Effects of SNPs on the binding of TF [gain (+) or loss (-)].
| TFs | Number | Lead SNPs | Linked SNPs | |
|---|---|---|---|---|
| NFATC2 | + | 16 | rs344081,rs271170,rs4869739 rs4729260,rs16921914,rs9533095 rs9303521 | rs1741,rs1135999,rs11650567,rs17408318 rs17457484,rs4869739,rs638076,rs6904261 rs6962748 |
| - | 15 | rs1430742,rs2566755,rs1463104,rs2887571 | rs2124954,rs17154676,rs9309078 rs13345828,rs227421,rs11627052 rs11757289,rs399996,rs4335155,rs7221132 rs9466057 | |
| MEF2C | + | 10 | rs1463104,rs479336,rs9287237 rs6894139,rs1286083 | rs12474135,rs2124954,rs271171,rs2812415 rs6984675 |
| - | 11 | rs17509082,rs87938,rs10048146 rs6930633 | rs227427,rs4487685,rs4922787,rs1286079 rs9998083,rs1989565,rs158143 | |
| SOX9 | + | 10 | rs2707466,rs718766,rs1286083 rs2273061,rs1366594 | rs9383935,rs17013324,rs4922787,rs2707466 rs2536175 |
| - | 10 | rs13247600,rs479336 | rs9371552,rs11627052,rs1828720,rs7683315 rs11844519,rs271171,rs6932260,rs6744982 | |
| RUNX2 | + | 7 | rs7084921,rs3801387 | rs1471400,rs985296,rs11773399,rs11844519 rs11155797 |
| - | 4 | rs7932354 | rs9466058,rs2207491,rs6984675 | |
| ESR2 | + | 3 | - | rs9646629,rs11658881,rs219749 |
| - | 6 | rs1430740,rs6993813,rs7117858 rs2887571 | rs13177576,rs2490058 | |
| FOXA1 | + | 1 | rs1053051 | - |
| - | 4 | rs4729260 | rs9998083,rs7155014,rs7792993 | |
| STAT3 | + | 1 | - | rs11752730 |
| - | 3 | - | rs6465511,rs228768,rs3760891 | |
Effect of SNPs on the binding of miRNA (gain or loss).
| SNP/Gene | miRNA (loss) | miRNA (gain) |
|---|---|---|
| rs884205(A→C)/ | miR-3658 | |
| rs1026364(G→T)/ | miR-345-5p | |
| rs3204848(A→G)/ | miR-493-5p/miR-4718 | |
| rs3734805(A→C)/ | miR-641/3617-5p/miR-3915 | miR-4524b-3p/miR-4459 |
| rs6932260(T→C)/ | miR-16-2-3p/miR-195-3p/miR-656 | |
| rs6904261(G→A)/ | miR-4778-3p | |
| rs6932603(T→C)/ | miR-153/miR-544a | |
| rs9383935(C→T)/ | miR-4798-3p | miR-5197-5p |
| rs3734806(G→A)/ | miR-2964a-5p/miR-572 | |
| rs3757322(T→G)/ | miR-4274/miR-374b-3p | |
| rs1741(G→C)/ | miR -548t-5p/miR-4536-5p/miR-4796-3p/miR-548az-5p | |
| rs6498540(A→G) | miR-3156-3p | miR-1260a/miR-1260b |
| rs1121(G→A)/ | miR-550a-5p/miR-550a-3-5p/miR-1271-3p/miR-3064-5p/miR-6504-5p |
Fig 2GO annotation of osteoporosis GWAS-associated gene by PANTHER (A: Biological Process; B: Molecular Function; C: Cellular Component).
Pathway enrichment analysis of osteoporosis GWAS-associated genes.
| GO_ID | Term | Number of genes | p-value |
|---|---|---|---|
| hsa04310 | Wnt signaling pathway | 6 | 2.48E-03 |
| hsa05217 | Basal cell carcinoma | 4 | 8.49E-03 |
| hsa04340 | Hedgehog signaling pathway | 4 | 9.12E-03 |
Fig 3Protein-protein interaction network of osteoporosis GWAS-associated genes.
The nodes and edges represent the proteins (genes) and interactions, respectively. Green means neighborhood, red means gene fusion, mustard means textmining, black means coexpression, purple means experiments, and blue means cooccurence.
Fig 4The circle plot of GWAS3D for osteoporosis GWAS-SNPs based on all cell line and CEU population.
The red line indicated long-range interaction signals, and the intensity of interaction was represented by the width of the line. Interactive elements with significant SNP will start with ‘I_’.