Table 3

Pathways associated with different network modules.

Module


KEGG Pathway

1

2

3

4

5

6

7


Metabolism

Amino Acid Metabolism

Cysteine and methionine metabolism

7E-02

Glycine, serine and threonine metabolism

5E-02

Valine, leucine and isoleucine degradation

8E-03


Biosynthesis of Secondary Metabolites

Terpenoid backbone biosynthesis

8E-03


Carbohydrate Metabolism

Butanoate metabolism

7E-02

Inositol phosphate metabolism

1E-02

Propanoate metabolism

7E-02

Pyruvate metabolism

3E-02


Energy Metabolism

Reductive carboxylate cycle (CO2 fixation)

3E-02


Glycan Biosynthesis and Metabolism

Glycosaminoglycan degradation

2E-03

Glycosphingolipid biosynthesis - ganglio series

7E-02

Heparan sulfate biosynthesis

4E-02


Lipid Metabolism

Arachidonic acid metabolism

2E-02

Ether lipid metabolism

8E-02

Fatty acid elongation in mitochondria

2E-02

Fatty acid metabolism

3E-02

Glycerolipid metabolism

2E-03

Glycerophospholipid metabolism

1E-02

Sphingolipid metabolism

2E-02

Steroid biosynthesis

8E-05

Synthesis and degradation of ketone bodies

3E-02


Metabolism of Cofactors and Vitamins

Nicotinate and nicotinamide metabolism

5E-04

One carbon pool by folate

7E-02


Metabolism of Other Amino Acids

Selenoamino acid metabolism

4E-02


Xenobiotics Biodegradation and Metabolism

Benzoate degradation via CoA ligation

6E-02

Caprolactam degradation

8E-03


Genetic Information Processing

Folding, Sorting and Degradation

RNA degradation

2E-02


Environmental Information Processing

Signal Transduction

ErbB signaling pathway

2E-02

Hedgehog signaling pathway

4E-05

Jak-STAT signaling pathway

1E-02

MAPK signaling pathway

8E-02

5E-03

2E-03

mTOR signaling pathway

1E-02

Notch signaling pathway

4E-03

Phosphatidylinositol signaling system

4E-02

TGF-beta signaling pathway

4E-02

1E-02

VEGF signaling pathway

6E-02

9E-03

Wnt signaling pathway

1E-02

1E-04


Signaling Molecules and Interaction

Cell adhesion molecules (CAMs)

3E-02

Cytokine-cytokine receptor interaction

4E-03

6E-02

ECM-receptor interaction

1E-02


Cellular Processes

Cell Communication

Adherens junction

3E-02

Focal adhesion

1E-02

5E-04

3E-02

Tight junction

4E-04


Cell Growth and Death

Apoptosis

2E-02

Cell cycle

8E-02

p53 signaling pathway

3E-02


Cell Motility

Regulation of actin cytoskeleton

9E-04


Circulatory System

Vascular smooth muscle contraction

4E-06


Development

Axon guidance

7E-02

7E-02


Endocrine System

Adipocytokine signaling pathway

3E-02

2E-06

GnRH signaling pathway

9E-02

Insulin signaling pathway

2E-05

1E-02

7E-05


Immune System

Antigen processing and presentation

8E-02

B cell receptor signaling pathway

8E-03

Chemokine signaling pathway

2E-09

Complement and coagulation cascades

1E-02

Fc epsilon RI signaling pathway

4E-02

Fc gamma R-mediated phagocytosis

1E-03

Leukocyte transendothelial migration

1E-02

T cell receptor signaling pathway

2E-03

Toll-like receptor signaling pathway

2E-02

9E-02


Nervous System

Neurotrophin signaling pathway

7E-06


Transport and Catabolism

Endocytosis

3E-04


Human Diseases

Cancers

Acute myeloid leukemia

2E-02

Basal cell carcinoma

3E-05

Chronic myeloid leukemia

8E-03

9E-03

Colorectal cancer

1E-02

4E-02

3E-02

Endometrial cancer

6E-02

1E-02

Glioma

1E-01

Pancreatic cancer

3E-02

Pathways in cancer

3E-07

3E-03

Prostate cancer

4E-02

Renal cell carcinoma

3E-02

Small cell lung cancer

1E-02

Thyroid cancer

5E-03


Circulatory Diseases

Arrhythmogenic right ventricular cardiomyopathy (ARVC)

6E-02

Hypertrophic cardiomyopathy (HCM)

2E-04


Infectious Diseases

Epithelial cell signaling in Helicobacter pylori infection

2E-05


Neurodegenerative Diseases

Amyotrophic lateral sclerosis (ALS)

6E-02


With genes in each module of the network, pathway enrichment analysis was performed using one-sided Fisher exact test. The significance level of p-value is represented by regular (0.01~0.1), bold (0.0001~0.01) and bold-italic (<0.0001) fonts.

Cho et al. BMC Medical Genomics 2011 4:8   doi:10.1186/1755-8794-4-8

Open Data