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Table 3 The enriched pathways of the responsive gene modules of VEGF 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)
Chronic myeloid leukemia 0.25(6.20), 1 a 0.19(5.32), 2 0.07(0.72), 4 0.19(3.67), 3
TGF-beta signaling pathway 0.23(5.88), 1 0.14(3.40), 2 0.04(-0.53), 4 0.14(2.20), 3
Adherens junction 0.22(4.74), 1 0.10(1.73), 3 0.12(2.50), 2 0.12(1.23), 4
Pancreatic cancer 0.19(3.99), 2 0.18(4.76), 1 0.06(0.13), 4 0.17(2.76), 3
Neurodegenerative Diseases 0.24(3.75), 1 0.12(1.57), 2 0.03(-0.61), 4 0.12(0.81), 3
Focal adhesion 0.13(3.66), 1 0.08(1.72), 2 0.07(1.16), 4 0.11(1.71), 3
Cell cycle 0.16(3.51), 2 0.16(5.02), 1 0.01(-1.89), 4 0.05(-1.27), 3
Long-term potentiation 0.19(3.47), 1 0.10(1.52), 2 0.05(-0.05), 4 0.08(0.13), 3
Wnt signaling pathway 0.14(3.24), 1 0.06(0.35), 2 0.04(-0.74), 3 0.05(-1.03), 4
Prostate cancer 0.16(3.15), 2 0.15(3.74), 1 0.06(0.38), 4 0.10(0.72), 3
SNARE interactions in vesicular transport 0.23(3.11), 1 0.00(-1.43), 4 0.00(-1.38), 3 0.06(-0.31), 2
Renal cell carcinoma 0.17(3.09), 1 0.09(1.44), 3 0.08(0.93), 4 0.14(1.90), 2
Notch signaling pathway 0.21(3.04), 2 0.27(5.60), 1 0.03(-0.54), 4 0.12(0.89), 3
Acute myeloid leukemia 0.17(2.74), 2 0.17(3.73), 1 0.06(0.15), 4 0.13(1.43), 3
Endometrial cancer 0.17(2.47), 2 0.17(3.42), 1 0.06(0.29), 4 0.10(0.58), 3
Dorso-ventral axis formation 0.22(2.43), 2 0.22(3.11), 1 0.09(0.71), 3 0.09(0.06), 4
Apoptosis 0.13(1.95), 2 0.04(-0.77), 3 0.03(-1.19), 4 0.19(3.63), 1
Fc epsilon RI signaling pathway 0.09(0.57), 4 0.08(0.70), 3 0.17(4.40), 1 0.15(2.23), 2
Small cell lung cancer 0.06(-0.54), 3 0.11(2.27), 2 0.04(-0.70), 4 0.20(4.31), 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).