Table 1.

Differentially expressed genes and gene subsets found in microarray analysis of EBRGs and NBRGs

Upregulated genes by subtypeLog2 (fold change)Adjusted PRef.
EBRG genes (n = 5; relative to 4 NBRGs)
 MAPK43.30.01
 MAPK102.10.01
 NCAM-11.80.03
 Aquaporin 43.30.02
NBRG genes (n = 4; relative to 5 EBRGs)
 Integrin α51.40.03
 Fibronectin12.20.01
 Laminin, alpha 4 chain1.20.04
 Platelet-derived growth factor receptor β (PDGFRβ)1.60.03
EBRG genes (n = 5; relative to paired pre-EBRGs)
 Angiopoietin 2–1.30.0001(45)
 Integrin β1–1.00.0015(46)
 Integrin α8–1.00.0010(47)
NBRG genes (n = 4; relative to paired pre-NBRGs)
 Fibronectin11.40.0006(40)
 Neutrophin 31.50.001(43)
 Integrin α51.00.002(44)
 TWIST11.00.002(40)
 PDGFRβ1.10.002(28)
 CXCL121.10.002(42)
 Interleukin 61.10.002(48)
GSEAQ
 EBRGs (n = 5; upregulated relative to 5 NBRGs)
  CNS development1 × 10−5
 NBRGs (n = 4; upregulated relative to 4 EBRGs)
  Regulation of wound healing3 × 10−3
  Collagen biosynthetic process9 × 10−3
  Collagen metabolic process3 × 10−3
  Collagen fibril organization2 × 10−3
  Inflammation mediated by chemokine and cytokine signaling pathways2 × 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.