Differentially expressed genes and gene subsets found in microarray analysis of EBRGs and NBRGs
| Upregulated genes by subtype | Log2 (fold change) | Adjusted P | Ref. |
|---|---|---|---|
| EBRG genes (n = 5; relative to 4 NBRGs) | |||
| MAPK4 | 3.3 | 0.01 | |
| MAPK10 | 2.1 | 0.01 | |
| NCAM-1 | 1.8 | 0.03 | |
| Aquaporin 4 | 3.3 | 0.02 | |
| NBRG genes (n = 4; relative to 5 EBRGs) | |||
| Integrin α5 | 1.4 | 0.03 | |
| Fibronectin1 | 2.2 | 0.01 | |
| Laminin, alpha 4 chain | 1.2 | 0.04 | |
| Platelet-derived growth factor receptor β (PDGFRβ) | 1.6 | 0.03 | |
| EBRG genes (n = 5; relative to paired pre-EBRGs) | |||
| Angiopoietin 2 | –1.3 | 0.0001 | (45) |
| Integrin β1 | –1.0 | 0.0015 | (46) |
| Integrin α8 | –1.0 | 0.0010 | (47) |
| NBRG genes (n = 4; relative to paired pre-NBRGs) | |||
| Fibronectin1 | 1.4 | 0.0006 | (40) |
| Neutrophin 3 | 1.5 | 0.001 | (43) |
| Integrin α5 | 1.0 | 0.002 | (44) |
| TWIST1 | 1.0 | 0.002 | (40) |
| PDGFRβ | 1.1 | 0.002 | (28) |
| CXCL12 | 1.1 | 0.002 | (42) |
| Interleukin 6 | 1.1 | 0.002 | (48) |
| GSEA | Q | ||
| EBRGs (n = 5; upregulated relative to 5 NBRGs) | |||
| CNS development | 1 × 10−5 | ||
| NBRGs (n = 4; upregulated relative to 4 EBRGs) | |||
| Regulation of wound healing | 3 × 10−3 | ||
| Collagen biosynthetic process | 9 × 10−3 | ||
| Collagen metabolic process | 3 × 10−3 | ||
| Collagen fibril organization | 2 × 10−3 | ||
| Inflammation mediated by chemokine and cytokine signaling pathways | 2 × 10−3 | ||
| EBRGs (n = 5; altered relative to pre-EBRGs) | |||
| Cell junctions (upregulated) | 3 × 10−4 | ||
| Intermediate filaments (downregulated) | 1 × 10−4 | ||
| Fibrillar collagen (downregulated) | 7 × 10−3 | ||
| NBRGs (n = 4; altered relative to pre-NBRGs) | |||
| Integrin signaling pathway (upregulated) | 5 × 10−9 | ||
| Extracellular matrix (upregulated) | 3 × 10−11 | ||
| Collagen (upregulated) | 4 × 10−5 | ||
| Integrin binding (upregulated) | 9 × 10−4 | ||
| Metallopeptidase activity (upregulated) | 9.5 × 10−3 | ||
| Metalloendopeptidase activity (upregulated) | 8 × 10−3 | ||
| Response to wounding (upregulated) | 8 × 10−10 | ||
| Regulation of cell migration (upregulated) | 8 × 10−7 | ||
| Regulation of cell motility (upregulated) | 8 × 10−7 | ||
| Cell-matrix adhesion (upregulated) | 8 × 10−6 | ||
| Chemotaxis (upregulated) | 1 × 10−4 | ||
| Wnt receptor signaling pathway (upregulated) | 8 × 10−4 | ||
| M phase (downregulated) | 5 × 10−4 | ||
| M phase of mitotic cell cycle (downregulated) | 2 × 10−3 | ||
NOTE: For comparisons of expression of specific genes in EBRGs versus NBRGs, P values adjusted for multiple testing by controlling the false discovery rate are listed for representative genes with adjusted P < 0.05. For comparisons of EBRGs and NBRGs to pretreatment specimens (pre-EBRGs and pre-NBRGs), shown are representative genes (negative log FC = downregulated; positive log FC = upregulated) with raw P < 0.002, along with supportive references. For gene subsets, Q values are adjusted for false discovery and representative subsets with Q < 0.01 are shown.
Abbreviations: Ref = Reference.