Table 3

Biological pathways activated by hypomethylation

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


Pathways listed are all pathways regulated by hypermethylated and downregulated genes, determined by Pathway Express corrected p-value < 0.05.

§ Pathway enrichment p-values were calculated using a one-tail Fisher's exact test. Asterisks show p-value < 0.05

Li et al. BMC Medical Genomics 2009 2:34   doi:10.1186/1755-8794-2-34

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