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Table 3 Biological pathways activated by hypomethylation

From: Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer

Pathways Upregulated genes
(1036)
Hypomethylated and upregulated genes
(55)
Fisher's Exact Test p-values§
  Input genes in pathway Corrected p-value Input genes in pathway Genes in pathway Corrected p-value  
Glioma 6 1.60E-02 3 PIK3R3, PDGFRA, E2F1 8.69E-05 0.003*
Melanoma 5 6.00E-02 3 PIK3R3, PDGFRA, E2F1 3.91E-04 0.001*
Pancreatic cancer 8 3.30E-02 3 PIK3R3, E2F1, TGFBR2 1.10E-03 0.006*
Prostate cancer 9 3.80E-02 3 PIK3R3, PDGFRA, E2F1 1.20E-03 0.009*
Colorectal cancer 6 1.84E-01 3 PIK3R3, E2F1, TGFBR2 1.50E-03 0.003*
Chronic myeloid leukemia 6 1.75E-01 3 PIK3R3, E2F1, TGFBR2 2.50E-03 0.003*
Non-small cell lung cancer 2 6.00E-01 2 PIK3R3, E2F1 2.46E-02 0.003*
Phosphatidylinositol signaling system 4 5.32E-07 1 PIK3R3 2.23E-12 0.196
Gap junction 5 4.12E-02 1 PDGFRA 1.06E-05 0.239
Focal adhesion 17 8.76E-03 2 PIK3R3, PDGFRA 9.13E-05 0.226
MAPK signaling pathway 8 5.90E-02 2 PDGFRA, TGFBR2 9.73E-05 0.063
TGF-beta signaling pathway 6 1.13E-01 1 TGFBR2 5.67E-04 0.280
Adherens junction 7 4.44E-02 1 TGFBR2 6.41E-03 0.318
Regulation of actin cytoskeleton 15 8.57E-02 3 PIK3R3, PDGFRA, MSN 6.73E-03 0.051
Calcium signaling pathway 5 2.65E-01 1 PDGFRA 1.70E-02 0.239
Leukocyte transendothelial migration 9 3.98E-02 2 PIK3R3, MSN 1.92E-02 0.078
  1. Pathways listed are all pathways regulated by hypermethylated and downregulated genes, determined by Pathway Express corrected p-value < 0.05.
  2. § Pathway enrichment p-values were calculated using a one-tail Fisher's exact test. Asterisks show p-value < 0.05