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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