| Literature DB >> 30483788 |
Peiyan Huang1, Jun Gu1, Junguo Wu1, Lei Geng1, Yang Hong1, Siqun Wang1, Minghai Wang1.
Abstract
The aim of the present study was to identify genes and functional pathways associated with meniscal injuries affected by age or body mass index (BMI) using microarray analysis. The GSE45233 gene expression dataset with 12 injured meniscus samples associated with age and BMI and GSE66635 dataset with 12 injured and 12 normal meniscus samples were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified based on age or BMI in GSE45233. DEGs between injured and normal meniscus samples in GSE66635 were also identified. Common DEGs between GSE45233 and GSE66635 were identified as feature genes associated with age or BMI, followed by protein‑protein interaction (PPI) network and functional pathway enrichment analyses for the feature genes. Finally, the GSE51588 genome‑wide expression profile was then downloaded from the GEO database to validate the results. A total of 1,328 DEGs were identified. Of these, 28 age‑associated and 20 BMI‑associated meniscal injury genes were obtained. B‑cell lymphoma‑2 (Bcl‑2) and matrix metalloproteinase‑14 were identified as hub genes in the PPI networks. Functional pathway enrichment analysis revealed that vascular endothelial growth factor A (VEGFA), transferrin (TF) and Bcl‑2 were involved in the hypoxia‑inducible factor 1 signaling pathway. TF was involved in the mineral absorption function pathway associated with BMI. Additionally, TF and VEGFA were identified to be overlapping candidate genes of GSE45233 and GSE66635, and DEGs in GSE51588. Therefore, VEGFA, TF, and Bcl‑2 may be important genes for human meniscal injuries. Additional evaluations of these results are required.Entities:
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Year: 2018 PMID: 30483788 PMCID: PMC6297773 DOI: 10.3892/mmr.2018.9685
Source DB: PubMed Journal: Mol Med Rep ISSN: 1791-2997 Impact factor: 2.952
Feature genes in age and body mass index groups.
| A, Age group | ||
|---|---|---|
| Gene | P-value | log2FC |
| S100A1 | 0.0004 | −5.64 |
| BARX2 | 0.0096 | −2.95 |
| IGFBP1 | 0.0341 | −2.46 |
| HAPLN1 | 0.0031 | −2.21 |
| DIXDC1 | 0.0123 | −2.01 |
| FGFBP2 | 0.0381 | −1.92 |
| FBLN7 | 0.0076 | −1.81 |
| VEGFA | 0.0173 | −1.66 |
| GREM1 | 0.0171 | −1.56 |
| TF | 0.0281 | −1.40 |
| BCL2 | 0.0345 | −1.30 |
| DCHS1 | 0.0020 | −1.29 |
| SMOC1 | 0.0042 | −1.23 |
| CAPN6 | 0.0167 | −1.20 |
| PTGES | 0.0352 | −1.08 |
| VIT | 0.0459 | 1.00 |
| LYZ | 0.0258 | 1.23 |
| FGL2 | 0.0033 | 1.24 |
| CCNB1 | 0.0030 | 1.31 |
| PBK | 0.0043 | 1.39 |
| BST2 | 0.0102 | 1.46 |
| CTSS | 0.0222 | 1.48 |
| HTRA4 | 0.0068 | 1.51 |
| DDHD1 | 0.0093 | 1.55 |
| TSPAN7 | 0.0007 | 1.57 |
| CALCRL | 0.0198 | 2.61 |
| EMCN | 0.0171 | 6.40 |
| CD36 | 0.0010 | 9.33 |
| EMCN | 0.0169 | −6.40 |
| FRY | 0.0353 | −4.20 |
| EDNRA | 0.0084 | −3.18 |
| MFAP2 | 0.0304 | −2.26 |
| CXCL12 | 0.0113 | −2.19 |
| ABHD2 | 0.0010 | −1.86 |
| EYA4 | 0.0339 | −1.79 |
| ARHGAP11B | 0.0145 | −1.57 |
| MKL2 | 0.0260 | −1.41 |
| MMP14 | 0.0398 | −1.26 |
| ISLR | 0.0121 | −1.18 |
| DIXDC1 | 0.0150 | 1.03 |
| BTC | 0.0212 | 1.14 |
| RCAN1 | 0.0191 | 1.34 |
| TF | 0.0325 | 1.45 |
| CST6 | 0.0397 | 1.48 |
| RAD51AP2 | 0.0007 | 1.58 |
| KAL1 | 0.0098 | 2.40 |
| S100A8 | 0.0042 | 2.74 |
| IGFBP1 | 0.0157 | 2.95 |
FC, fold change.
Figure 1.Comparison of the average expression levels between groups of feature genes. (A) A t-test of the average expression level of feature genes was performed. (B) Heat map of bidirectional hierarchical clustering for feature genes in the age group. Comparison of the average expression levels between groups of feature genes. (C) Heat map of bidirectional hierarchical clustering for feature genes in the body mass index group.
Figure 2.Scatter plots of support vector machines classification of the samples. (A) Age and (B) body mass index groups are presented. The orange color represents the young and obese samples. The green color represents old and lean samples. The x-axis and y-axis represent the sample position vector coordinates according to the classifier.
Figure 3.PPI networks of feature genes and network topology analysis. (A) PPI network constructed based on the feature genes in the age group. (B) PPI network constructed based on the feature genes in the BMI group. The yellow color represents upregulated genes and the blue color represents downregulated genes. The young group serves as the control in the age group, and the lean group serves as the control in the BMI group. The pink color represents the remaining interactional genes, with the exception of the feature genes. PPI, protein-protein interaction; BMI, body mass index.
Figure 4.Node degree distribution of the feature genes. (A) Node degree distribution of the age group network. (B) Node degree distribution of the body mass index group network.
List of top 10 highest degree nodes of the age and body mass index groups.
| A, Age group | |||
|---|---|---|---|
| Gene | P-value | log2FC | Degree |
| BCL2 | 0.0345 | −1.30 | 74 |
| CCNB1 | 0.0030 | 1.31 | 30 |
| S100A1 | 0.0004 | −5.64 | 18 |
| VEGFA | 0.0173 | −1.66 | 18 |
| TF | 0.0281 | −1.40 | 14 |
| CD36 | 0.0010 | 9.33 | 13 |
| PBK | 0.0043 | 1.39 | 12 |
| CTSS | 0.0222 | 1.48 | 8 |
| HAPLN1 | 0.0031 | −2.21 | 7 |
| CALCRL | 0.0198 | 2.61 | 6 |
| MMP14 | 0.0398 | −1.26 | 20 |
| S100A8 | 0.0042 | 2.74 | 16 |
| TF | 0.0325 | 1.45 | 14 |
| CXCL12 | 0.0113 | −2.19 | 7 |
| EDNRA | 0.0084 | −3.18 | 6 |
| IGFBP1 | 0.0157 | 2.95 | 5 |
| MFAP2 | 0.0304 | −2.26 | 5 |
| RCAN1 | 0.0191 | 1.34 | 5 |
| BTC | 0.0212 | 1.14 | 4 |
| MKL2 | 0.0260 | −1.41 | 3 |
Pathways associated with feature genes in the age and BMI groups.
| Group | Pathway | ID | P-value | Genes |
|---|---|---|---|---|
| Age | HIF-1 signaling pathway | hsa04066 | 0.002013 | VEGFA, TF, BCL2 |
| BMI | Mineral absorption | hsa04978 | 0.043813 | TF |
HIF-1, hypoxia-inducible factor 1; VEGFA, vascular endothelial growth factor A; TF, transferrin; BCL2, B-cell lymphoma 2; BMI, body mass index.
Overlapping genes between candidate genes and differentially expressed genes in GSE51588.
| Differentially expressed genes | Candidate genes in GSE51588 | ||||
|---|---|---|---|---|---|
| Gene name | P-value | logFC | Type | P-value | logFC |
| TF | 2.81×10-2 | −1.40 | Age | 3.20×10-3 | −0.56 |
| VEGFA | 1.73×10-2 | −1.66 | Age | 7.95×10-3 | −0.62 |
| BST2 | 1.02×10-2 | 1.46 | Age | 6.25×10-3 | 0.64 |
| EMCN | 1.71×10-2 | 6.40 | Age | 1.23×10-5 | 0.65 |
| VIT | 4.59×10-2 | 1.00 | Age | 4.17×10-5 | 0.70 |
| ABHD2 | 9.91×10-4 | −1.86 | BMI | 2.09×10-2 | −0.56 |
| ARHGAP11B | 1.45×10-2 | −1.57 | BMI | 1.19×10-2 | −0.72 |
| BTC | 2.12×10-2 | 1.14 | BMI | 4.12×10-3 | 1.13 |
| DIXDC1 | 1.50×10-2 | 1.03 | BMI | 2.27×10-7 | 0.63 |
| KAL1 | 9.84×10-3 | 2.40 | BMI | 1.39×10-3 | 0.95 |
| RAD51AP2 | 6.60×10-4 | 1.58 | BMI | 4.94×10-2 | 0.37 |
BMI, body mass index.