Skip to main content

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).
Back to article page

BMC Systems Biology

ISSN: 1752-0509

Contact us