Table 2

Transcription regulation analysis by GeneGo's MetaCore

No

Network

GO Processes

Total nodes

Root nodes

p-Value


1

ESR1 (nuclear)

positive regulation of retinoic acid receptor signaling pathway (16.7%; 1.463e-03), negative regulation of mitosis (16.7%; 2.194e-03), epithelial cell maturation (16.7%; 2.559e-03), regulation of retinoic acid receptor signaling pathway (16.7%; 2.925e-03), melanosome localization (16.7%; 4.019e-03)

6

5

3.20E-18


2

HNF4-alpha

negative regulation of protein import into nucleus, translocation (16.7%; 7.318e-04), negative regulation of tyrosine phosphorylation of Stat5 protein (16.7%; 1.463e-03), regulation of protein import into nucleus, translocation (16.7%; 1.829e-03), ornithine metabolic process (16.7%; 2.559e-03), positive regulation of gluconeogenesis (16.7%; 2.559e-03)

6

5

3.20E-18


3

Androgen receptor

prostate gland development (40.0%; 4.905e-06), male somatic sex determination (20.0%; 3.050e-04), somatic sex determination (20.0%; 6.099e-04), gland development (40.0%; 7.323e-04), urogenital system development (40.0%; 7.845e-04)

5

4

1.44E-14


4

HNF1-alpha

glucose homeostasis (66.7%; 5.376e-05), carbohydrate homeostasis (66.7%; 5.376e-05), epithelial cell maturation (33.3%; 1.280e-03), bile acid biosynthetic process (33.3%; 1.646e-03), paraxial mesoderm formation (33.3%; 1.829e-03)

3

2

1.89E-07


5

HNF3-beta

neuron fate specification (66.7%; 2.343e-06), positive regulation of neuron differentiation (66.7%; 6.156e-06), neuron fate commitment (66.7%; 2.409e-05), cell fate specification (66.7%; 3.555e-05), epithelial cell differentiation (66.7%; 6.683e-05)

3

2

1.89E-07


Transcription regulation analysis using GeneGo's MetaCore generates sub-networks centered on transcription factors using the 17 genes discovered by Backward Chaining Rule Induction (Figure 6). Sub-networks are ranked by a p-value and interpreted in based on Gene Ontology (GO) categories.

Sanga et al. BMC Medical Genomics 2009 2:59   doi:10.1186/1755-8794-2-59

Open Data