Table 2

Significant GO processes

GO term

Description

Permutation

p-value (weighted approach)

Permutation

p-value (unweighted approach)

GO:0000186†

Activation of MAP kinase activity, especially during sporulation

<1.0 × 10^–6

4.0 × 10^–5

GO:0001569†*

Branching involved in blood vessel morphogenesis

<1.0 × 10^–6

<1.0 × 10^–6

GO:0001666†*

Response to lowered oxygen tension

<1.0 × 10^–6

1.0 × 10^–6

GO:0001938†*

Up-regulation of endothelial cell proliferation

<1.0 × 10^–6

<1.0 × 10^–6

GO:0002040†*

Sprouting angiogenesis

<1.0 × 10^–6

<1.0 × 10^–6

GO:0006355†*

Regulation of cellular transcription, DNA-dependent

<1.0 × 10^–6

<1.0 × 10^–6

GO:0006916*

Anti-apoptosis

7.5 × 10^–5

1.0 × 10^–6

GO:0006940†*

Any process that modulates the frequency, rate, or extent of smooth muscle contraction

<1.0 × 10^–6

<1.0 × 10^–6

GO:0006952 †

Defense/immunity protein activity

8.0 × 10^–6

1.9 × 10^–5

GO:0007169†*

Transmembrane receptor protein tyrosine kinase signaling pathway

<1.0 × 10^–6

<1.0 × 10^–6

GO:0008152†

Metabolic process

3.0 × 10^–6

2.2 × 10^–5

GO:0010595†*

Up-regulation of endothelial cell migration

<1.0 × 10^–6

7.0 × 10^–6

GO:0030097†

Blood cell formation

<1.0 × 10^–6

(a)

*GO:0030522†*

Intracellular receptor-mediated signaling pathway

<1.0 × 10^–6

<1.0 × 10^–6

GO:0030949†*

Up-regulation of vascular endothelial growth factor (VEGF) receptor signaling pathway

<1.0 × 10^–6

<1.0 × 10^–6

GO:0043129†*

Surfactant homeostasis

<1.0 × 10^–6

1.1 × 10^–5

GO:0045446†

Endothelial cell differentiation

<1.0 × 10^–6

(a)

GO:0045745*

Positive regulation of G-protein coupled receptor protein signaling pathway

6.425 × 10^–2

1.2 × 10^–5

GO:0048286†*

Lung alveolus development

<1.0 × 10^–6

5.0 × 10^–6

GO:0048661†*

Up-regulation of smooth muscle cell proliferation

<1.0 × 10^–6

<1.0 × 10^–6

GO:0050927†

Up-regulation of positive chemotaxis

<1.0 × 10^–6

(a)

GO:0051894†

Up-regulation of focal adhesion formation

<1.0 × 10^–6

(a)

GO:0055074†

Regulation of calcium ion concentration

<1.0 × 10^–6

(a)

† Pathways (processes) that are significant using the weighted approach.

* Pathways (processes) that are significant using the unweighted approach.

^a Once 100 permuted data sets were found to have a larger Wald statistic for a given process than that observed in the original (unpermuted) data set, that process was deemed nonsignificant and further permutations were not performed.

Xing et al. BMC Proceedings 2011 5(Suppl 9):S6   doi:10.1186/1753-6561-5-S9-S6