Table 1

Gene Ontology enrichment analysis for six out of seven effective genes whose overexpression perturbed the mES transcriptome in a statistically significant manner

Gene

Gene Ontology term

FDR

Fold enrichment

Reference


Runx1

Negative regulation of progression through cell cycle

2.8

1.5

[60,61]

Positive regulation of cell proliferation

0.5

1.5

[60,61]

Vasculature development

0.1

1.5

[62,63]

Blood vessel development

0.2

1.5

[62,63]

Blood vessel morphogenesis

0.1

1.6

[62,63]

Angiogenesis

0.1

1.6

[62,63]

Regulation of myeloid cell differentiation

0.8

2.1

[63]

Skeletal development

0.2

1.5

[64]

Skeletal morphogenesis

1.7

2.5

[64]

Regulation of cell differentiation

0.0

1.7

[65]

Erg

Anatomical structure formation

0.2

1.5

[66]

Angiogenesis

0.0

1.6

[67,68]

Regulation of cell differentiation

0.8

1.5

[67,68]

Cell growth

2.3

1.5

[67,68]

Regulation of cell migration

1.3

1.8

[67,68]

Negative regulation of transcription, DNA-dependent

0.5

1.5

[68]

Nrip1

Muscle cell differentiation

2.0

4.3

[69]

Nervous system development

0,1

2.0

[70]

Negative regulation of transcription, DNA-dependent

3.6

2.6

[71]

Olig2

Organ morphogenesis

0.5

1.6

[72,73]

Placenta development

1.3

4.3

[74]

Negative regulation of progression through cell cycle

3.6

2.1

[75]

Pdxk

Cellular macromolecule catabolic process

2.0

2.7

[76,77]

Cellular carbohydrate metabolic process

0.0

4.1

[76,77]

Amino acid biosynthetic process

0.6

7.3

[78]

Aire

Cell morphogenesis

0.0

1.6

[79]

Regulation of progression through cell cycle

0.0

1.7

[79]

Regulation of cell differentiation

0.4

1.9

[79]

Cell migration

4.0

1.5

[80]


Perturbation of the mES transcriptome was as assessed by microarray analysis. GO analysis was performed on the list of differentially expressed genes using the DAVID tool, restricting the output to biological process terms of levels 4 and 5, with a significance threshold FDR < 5% and fold enrichment ≥ 1.5%. Supporting references confirming GO analysis are reported in the 'References' column.

De Cegli et al. Genome Biology 2010 11:R64   doi:10.1186/gb-2010-11-6-r64

Open Data