TABLE 4.
List of 18 genes selected from preceding analyses for confirmation by qPCR. The first six genes were suggested by the WGCNA method with GO annotation (White GO module), while the remaining 12 genes were identified by DESeq2 in combination with either GSEA or CPDB pathway analysis. Five genes (CIB1, MMP2, TNFRSF12A, FGF16, FGFRL1) have been chosen by the WGCNA method only and not by DESeq2, indicating those genes from the most highly correlated module may still be important in angiogenesis pathways, despite not being significantly differentially expressed.
| Gene symbol | Gene name | Module | Evidence |
|---|---|---|---|
| CIB1 | Calcium and integrin binding 1 | White | White GO |
| MMP2 | Matrix metallopeptidase 2 | White | White GO |
| SERPINE1 | Serpin family E member 1 | White | White GO/GSEA/CPDB |
| TNFRSF12A | TNF receptor superfamily member 12A | White | White GO |
| FGF16 | Fibroblast growth factor 16 | White | White GO |
| FGFRL1 | Fibroblast growth factor receptor-like 1 | White | White GO |
| SPARC | Secreted protein acidic and cysteine rich | Purple | GSEA |
| PDGFA | Platelet derived growth factor subunit A | palevioletred3 | GSEA/CPDB |
| SMOC1 | SPARC related modular calcium binding 1 | palevioletred2 | GSEA |
| GDF3 | Growth differentiation factor 3 | navajowhite2 | GSEA |
| TGFBR2 | Transforming growth factor beta receptor 2 | Lightyellow | GSEA/CPDB |
| PDGFRB | Platelet derived growth factor receptor beta | Darkmagenta | GSEA/CPDB |
| CYR61 | Cysteine rich angiogenic inducer 61 | Darkgrey | GSEA/CPDB |
| ITGB1 | Integrin subunit beta 1 | Black | GSEA |
| PDGFC | Platelet derived growth factor C | Black | GSEA |
| SLIT3 | Slit guidance ligand 3 | antiquewhite4 | GSEA |
| IL8(CXCL8) | C-X-C motif chemokine ligand 8 | Steelblue | GSEA/CPDB |
| EDN1 | Endothelin 1 | Steelblue | CPDB |