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Table 1 The enriched pathways of the responsive gene modules of TNF stimulated HUVECs identified by different methods.

From: Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis

Pathway ClustEx Meet/Min (z-score) jActiveModules Meet/Min (z-score) GXNA Meet/Min (z-score) FoldChange_2.0 Meet/Min (z-score)
Apoptosis 0.29(6.14), 1 a 0.22(4.00), 3 0.15(3.70), 4 0.28(4.31), 2
Adipocytokine signaling pathway 0.27(4.88), 1 0.15(1.39), 4 0.13(2.32), 3 0.26(3.16), 2
Prostate cancer 0.24(4.83), 2 0.27(5.52), 1 0.10(1.58), 3 0.16(0.96), 4
Notch signaling pathway 0.33(4.78), 2 0.18(1.58), 3 0.05(-0.24), 4 0.38(4.80), 1
Jak-STAT signaling pathway 0.20(4.75), 1 0.09(0.09), 4 0.07(0.83), 3 0.21(3.38), 2
Toll-like receptor signaling pathway 0.23(4.68), 2 0.20(3.49), 3 0.11(2.21), 4 0.31(5.16), 1
Small cell lung cancer 0.24(4.58), 1 0.21(3.78), 2 0.14(3.42), 3 0.21(2.57), 4
Huntington's disease 0.32(4.12), 2 0.36(4.57), 1 0.11(1.11), 3 0.14(0.25), 4
Chronic myeloid leukemia 0.23(4.05), 3 0.27(5.55), 1 0.19(4.91), 2 0.26(3.71), 4
Acute myeloid leukemia 0.26(4.04), 1 0.20(2.75), 2 0.13(2.32), 3 0.22(2.21), 4
Pancreatic cancer 0.23(4.02), 2 0.23(4.28), 1 0.10(1.40), 4 0.19(1.83), 3
Cell cycle 0.19(3.52), 2 0.23(5.53), 1 0.07(0.73), 4 0.15(0.74), 3
Neurodegenerative Diseases 0.28(3.49), 1 0.22(2.49), 2 0.03(-0.85), 4 0.17(0.73), 3
Epithelial cell signaling in Helicobacter pylori infection 0.23(3.40), 2 0.19(2.59), 4 0.16(3.18), 3 0.28(3.49), 1
Dorso-ventral axis formation 0.29(3.17), 1 0.25(2.61), 2 0.08(0.45), 4 0.25(1.85), 3
B cell receptor signaling pathway 0.21(3.06), 1 0.15(1.35), 4 0.11(1.82), 3 0.23(2.57), 2
Bladder cancer 0.23(2.85), 2 0.26(3.47), 1 0.13(1.70), 4 0.26(2.60), 3
T cell receptor signaling pathway 0.18(2.85), 3 0.09(-0.21), 4 0.13(3.26), 1 0.22(2.97), 2
Endometrial cancer 0.20(2.55), 2 0.22(3.16), 1 0.12(1.90), 3 0.12(-0.06), 4
Adherens junction 0.15(1.69), 2 0.21(3.38), 1 0.07(0.40), 3 0.11(-0.38), 4
Cytokine-cytokine receptor interaction 0.10(0.86), 3 0.05(-2.73), 4 0.08(1.25), 2 0.22(4.76), 1
TGF-beta signaling pathway 0.11(0.56), 4 0.15(1.83), 2 0.10(1.67), 3 0.28(4.30), 1
  1. a The rank of the pathway gene set enrichment of the compared methods according to the corresponding Meet/Min values' z-scores. The bold font denotes the enriched pathways (z-score > 3.0).