Table 1

Enrichment of GO categories in gene modules. Enrichment of GO categories in gene modules obtained from (a) the human transcriptome dataset and (b) the soft tissue tumor dataset. Only functional categories containing at least 6 genes and p-values less than 0.01 are reported.

a)

Factor

biological process

#genes

p-value


Factor 4 (726 genes)

Neurogenesis

43

0.0

Cell adhesion

33

1.30E-04

Transport

32

0.003

Synaptic transmission

31

0.0

Regulation of transcription, DNA-dependent

25

0.0

Central nervous system development

17

0.0

Small GTPase mediated signal transduction

17

4.70E-04

Potassium ion transport

11

0.008

Sodium ion transport

10

2.40E-04

Microtubule-based movement

9

0.0

Neuropeptide signaling pathway

8

2.40E-04

Regulation of apoptosis

8

0.009

ATP synthesis coupled proton transport

6

0.001

Microtubule polymerization

6

3.00E-05

Vesicle-mediated transport

6

7.70E-04

Factor 5 (414 genes)

Immune response

78

0.0

Signal transduction

47

0.0

Intracellular signaling cascade

29

0.0

Inflammatory response

26

0.0

Cellular defense response

21

0.0

Antigen presentation, endogenous antigen

18

0.0

Antigen processing, endogenous antigen via MHC class I

18

0.0

Proteolysis and peptidolysis

17

0.003

Cell motility

16

0.0

Cell surface receptor linked signal transduction

15

0.0

Chemotaxis

13

0.0

Positive regulation of l-kappaB kinase/NF-kappaB cascade

13

0.0

Regulation of apoptosis

12

0.0

Heterophilic cell adhesion

11

0.0

Antimicrobial tumoral response (sensu Vertebrata)

10

1.00E-05

Small GTPase mediated signal transduction

10

0.004

Anti-apoptosis

9

1.40E-04

Defense response

8

7.00E-05

Induction of apoptosis

8

0.002

Response to virus

7

0.0

Cell recognition

6

0.0

Integrin-mediated signaling pathway

6

2.90E-04

Factor 8 (339 genes)

Spermatogenesis

13

0.0

Transcription

11

0.0

Mitosis

6

0.002



b)

Factor

biological process

#genes

p-value

Factor 1 (546 genes)

Regulation of transcription, DNA-dependent

32

2.00E-05

Development

16

0.003

Neurogenesis

9

0.008

Transcription from Pol II promoter

7

0.007

Morphogenesis

6

0.002

Skeletal development

6

0.007

Chromosome organization and biogenesis (sensu Eukarya)

6

2.00E-05

Factor 2 (674 genes)

Signal transduction

32

7.00E-05

Immune response

30

0.0

Cell adhesion

24

0.0

Inflammatory response

17

0.0

Chemotaxis

16

0.0

Proteolysis and peptidolysis

15

0.002

Cell growth and/or maintenance

13

0.002

Cell-cell signaling

13

7.60E-04

Cell proliferation

13

0.002

Antimicrobial humoral response (sensu Vertebrata)

12

0.0

G-protein coupled receptor protein signaling pathway

11

3.80E-04

Cell motility

10

2.00E-05

Cellular defense response

9

0.0

Protein complex assembly

6

0.002

Positive regulation of cell proliferation

6

0.008

Cell-matrix adhesion

6

8.00E-05

Blood coagulation

6

0.001

Hetorophilic cell adhesion

6

0.002

Factor 3 (524 genes)

Signal transduction

22

0.004

Protein folding

6

0.002

Factor 4 (610 genes)

Metabolism

16

1.00E-04

Muscle development

11

1.00E-05

Electron transport

10

0.005

Carbohydrate metabolism

9

1.90E-04

Muscle contraction

9

0.0

DNA replication

6

0.002

Energy pathways

6

4.20E-04

Fatty acid metabolism

6

5.00E-05


Carmona-Saez et al. BMC Bioinformatics 2006 7:78   doi:10.1186/1471-2105-7-78

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