Table 1

Functional annotations enriched among genes upregulated* in BMP2⁺ cells compared to control cells in seven-day-old EBs

Category

Term

Count

p value

GOTERM_MF_5

Zinc ion binding

142

3.2E-16

GOTERM_CC_5

Nucleus

279

3.6E-12

GOTERM_BP_5

Transcription

128

2.5E-10

GOTERM_BP_5

Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism

121

5.5E-9

GOTERM_BP_5

Cellular protein metabolism

147

4.9E-8

GOTERM_MF_5

Binding

143

2.9E-7

GOTERM_MF_5

Metal ion binding

61

6.8E-7

GOTERM_MF_5

Transition metal ion binding

74

4.1E-6

GOTERM_MF_5

Cation binding

74

4.6E-6

GOTERM_MF_5

Ion binding

74

4.6E-6

GOTERM_BP_5

Biopolymer modification

83

1.3E-5

GOTERM_BP_5

Response to unfolded protein

12

2.5E-5

GOTERM_MF_5

ATP binding

84

6.8E-5

GOTERM_BP_5

Apoptosis

38

1.2E-4

GOTERM_CC_5

Intracellular membrane-bound organelle

225

2.4E-4

GOTERM_CC_5

Membrane-bound organelle

225

2.4E-4

GOTERM_BP_5

Regulation of protein kinase activity

12

3.1E-4

GOTERM_MF_5

Protein kinase activity

44

4.9E-4

KEGG_PATHWAY

MAPK signaling pathway

24

7.1E-4

GOTERM_BP_5

Nucleobase, nucleoside, nucleotide and nucleic acid metabolism

18

1.7E-3

GOTERM_BP_5

Regulation of programmed cell death

24

1.9E-3

GOTERM_CC_5

Intracellular

244

3.3E-3

GOTERM_BP_5

Response to protein stimulus

6

3.4E-3

GOTERM_CC_5

Vacuole

17

3.4E-3

GOTERM_BP_5

Phosphate metabolism

45

3.7E-3

GOTERM_BP_5

Cell death

16

4.1E-3

GOTERM_BP_5

Death

16

4.1E-3

GOTERM_BP_5

Programmed cell death

16

4.1E-3

GOTERM_BP_5

Negative regulation of cellular metabolism

17

5.6E-3

BIOCARTA

The information-processing pathway at the IFN-β enhancer

4

6.2E-3

GOTERM_BP_5

Regulation of apoptosis

22

6.7E-3

GOTERM_BP_5

Protein kinase cascade

17

6.8E-3

GOTERM_BP_5

Embryonic development

15

7.2E-3

GOTERM_MF_5

Nucleotide binding

41

8.9E-3

GOTERM_CC_5

Intracellular organelle

243

9.0E-3

GOTERM_CC_5

Organelle

243

9.0E-3

GOTERM_BP_5

Negative regulation of progression through cell cycle

10

9.3E-3

GOTERM_BP_5

Regulation of progression through cell cycle

24

9.7E-3

GOTERM_BP_5

Positive regulation of programmed cell death

12

1.2E-2

GOTERM_BP_5

Embryonic limb morphogenesis

7

1.5E-2

GOTERM_MF_5

Pyrophosphatase activity

29

2.1E-2

BIOCARTA

Regulation of transcriptional activity by PML

4

2.2E-2

GOTERM_BP_5

Cellular physiological process

112

2.3E-2

GOTERM_MF_5

Purine nucleotide binding

52

2.4E-2

GOTERM_BP_5

Embryonic development (sensu Mammalia)

7

2.7E-2

GOTERM_CC_5

Lytic vacuole

13

2.8E-2

GOTERM_BP_5

Negative regulation of protein kinase activity

5

2.8E-2

GOTERM_BP_5

Regulation of biological process

34

2.9E-2

GOTERM_CC_5

Cell

256

3.0E-2

GOTERM_BP_5

Regulation of cellular process

29

3.4E-2

GOTERM_BP_5

Regulation of protein biosynthesis

9

3.8E-2

GOTERM_MF_5

Transcription cofactor activity

9

3.8E-2

GOTERM_MF_5

Transcription factor binding

9

4.0E-2

GOTERM_BP_5

Negative regulation of programmed cell death

9

4.2E-2

GOTERM_BP_5

Protein catabolism

13

4.2E-2

GOTERM_BP_5

Regulation of gene expression, epigenetic

3

4.2E-2

GOTERM_MF_5

Protein kinase binding

6

4.3E-2

GOTERM_BP_5

Primary metabolism

35

4.5E-2

GOTERM_BP_5

RNA metabolism

22

4.5E-2

GOTERM_BP_5

Regulation of cellular biosynthesis

9

4.7E-2

GOTERM_MF_5

Guanyl nucleotide binding

14

4.8E-2

GOTERM_BP_5

Reproduction

11

4.8E-2

GOTERM_BP_5

Response to abiotic stimulus

13

4.8E-2

GOTERM_BP_5

Gene silencing

4

5.0E-2

KEGG_PATHWAY

Pantothenate and CoA biosynthesis

4

5.0E-2

GOTERM_BP_5

Physiological process

127

5.1E-2

GOTERM_BP_5

Bone resorption

3

5.2E-2

GOTERM_MF_5

Cysteine-type peptidase activity

9

5.2E-2

GOTERM_MF_5

Ligase activity

17

5.4E-2

GOTERM_BP_5

Response to chemical stimulus

11

5.4E-2

GOTERM_BP_5

Regulation of bone remodeling

4

5.6E-2

GOTERM_BP_5

Biopolymer catabolism

13

6.1E-2

KEGG_PATHWAY

Nitrogen metabolism

4

6.3E-2

GOTERM_BP_5

ER-nuclear signaling pathway

3

6.4E-2

GOTERM_BP_5

Regulation of protein metabolism

13

6.4E-2

GOTERM_CC_5

Nucleolus

12

7.1E-2

GOTERM_BP_5

Protein biosynthesis

30

7.3E-2

GOTERM_MF_5

Transcription corepressor activity

6

7.3E-2

GOTERM_BP_5

Intracellular receptor-mediated signaling pathway

3

7.6E-2

GOTERM_MF_5

Transcription regulator activity

9

7.7E-2

GOTERM_BP_5

Macromolecule biosynthesis

33

8.0E-2

GOTERM_BP_5

Positive regulation of cell proliferation

9

8.1E-2

GOTERM_BP_5

Embryonic hemopoiesis

2

8.2E-2

GOTERM_BP_5

Posttranscriptional gene silencing

2

8.2E-2

GOTERM_BP_5

RNA-mediated gene silencing

2

8.2E-2

GOTERM_BP_5

RNA-mediated posttranscriptional gene silencing

2

8.2E-2

GOTERM_MF_5

Glutaminase activity

2

8.4E-2

GOTERM_MF_5

Ubiquitin-protein ligase activity

16

8.4E-2

GOTERM_BP_5

Eye development

5

8.6E-2

BIOCARTA

Eukaryotic protein translation

3

9.0E-2

GOTERM_BP_5

Amino acid transport

6

9.1E-2

GOTERM_BP_5

Positive regulation of cell activation

5

9.2E-2

GOTERM_BP_5

Development

37

9.3E-2

*Change fold >2, Student's t-test p value < 0.01. Count indicates the number of genes in the functional annotation category. The p value is from gene enrichment in annotation terms calculated by the Fisher's exact t-test.

Doss et al. Genome Biology 2007 8:R184   doi:10.1186/gb-2007-8-9-r184