Table 5

Functional annotations (GO, KEGG, Biocarta) enriched in transcripts downregulated* in BMP2+ cells compared to control cells in seven-day-old EBs

Category

Term

Count

p value


GOTERM_BP_5

Development

82

3.6E-20

GOTERM_BP_5

Organ development

57

5.1E-19

GOTERM_BP_5

Morphogenesis

56

1.6E-16

GOTERM_BP_5

Cell differentiation

37

2.1E-11

GOTERM_BP_5

Blood vessel morphogenesis

25

1.7E-10

GOTERM_BP_5

Embryonic development

25

1.2E-8

GOTERM_BP_5

System development

30

1.9E-8

GOTERM_BP_5

Organ morphogenesis

27

2.3E-8

GOTERM_BP_5

Vasculature development

17

2.8E-8

GOTERM_BP_5

Tube development

18

5.8E-8

GOTERM_BP_5

Enzyme linked receptor protein signaling pathway

27

6.1E-8

GOTERM_BP_5

Cell migration

28

1.0E-7

GOTERM_BP_5

Blood vessel development

16

1.3E-7

GOTERM_BP_5

Nervous system development

25

5.5E-7

GOTERM_BP_5

Embryonic limb morphogenesis

12

1.8E-6

GOTERM_BP_5

Angiogenesis

17

3.7E-6

GOTERM_BP_5

Embryonic morphogenesis

14

6.7E-6

GOTERM_BP_5

Cell motility

21

7.3E-6

GOTERM_BP_5

Locomotion

21

8.7E-6

GOTERM_BP_5

Localization of cell

21

8.7E-6

GOTERM_BP_5

Neuron differentiation

24

1.1E-5

GOTERM_BP_5

Steroid biosynthesis

12

1.2E-5

GOTERM_BP_5

Brain development

16

1.9E-5

GOTERM_BP_5

Cell development

15

2.0E-5

GOTERM_BP_5

Alcohol catabolism

11

3.2E-5

GOTERM_BP_5

Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism

100

3.3E-5

GOTERM_BP_5

Tissue development

12

6.8E-5

GOTERM_BP_5

Axon guidance

12

6.8E-5

GOTERM_BP_5

Tube morphogenesis

10

7.1E-5

GOTERM_BP_5

Central nervous system development

10

8.5E-5

GOTERM_BP_5

Lipid biosynthesis

20

9.8E-5

GOTERM_BP_5

Monosaccharide metabolism

15

1.1E-4

GOTERM_BP_5

Regulation of biological process

41

1.4E-4

GOTERM_BP_5

Ossification

12

1.5E-4

GOTERM_BP_5

Transcription

99

1.6E-4

GOTERM_BP_5

Carbohydrate catabolism

11

2.2E-4

GOTERM_CC_5

Cell

203

2.6E-4

GOTERM_BP_5

Neural crest cell development

6

2.7E-4

GOTERM_BP_5

Regulation of development

11

2.9E-4

GOTERM_BP_5

Regulation of cellular process

35

3.1E-4

GOTERM_BP_5

DNA metabolism

34

3.4E-4

GOTERM_BP_5

Neuron morphogenesis during differentiation

16

3.4E-4

GOTERM_BP_5

Cellular macromolecule catabolism

21

3.5E-4

GOTERM_BP_5

Branching morphogenesis of a tube

7

4.1E-4

GOTERM_BP_5

Morphogenesis of a branching structure

7

4.1E-4

GOTERM_BP_5

Neurogenesis

15

4.3E-4

GOTERM_CC_5

Anchored to plasma membrane

5

4.8E-4

GOTERM_CC_5

Anchored to membrane

5

4.8E-4

GOTERM_BP_5

Cellular morphogenesis during differentiation

17

4.9E-4

GOTERM_BP_5

Pattern specification

10

4.9E-4

GOTERM_BP_5

Skeletal development

8

5.0E-4

GOTERM_BP_5

Limb morphogenesis

7

6.2E-4

GOTERM_BP_5

Appendage morphogenesis

7

6.2E-4

GOTERM_BP_5

Appendage development

7

6.2E-4

GOTERM_BP_5

Regulation of cell differentiation

9

8.5E-4

GOTERM_BP_5

Patterning of blood vessels

6

8.5E-4

GOTERM_BP_5

Vasculogenesis

6

8.5E-4

GOTERM_BP_5

Regulation of myeloid cell differentiation

4

1.1E-3

GOTERM_BP_5

Cellular carbohydrate metabolism

21

1.2E-3

GOTERM_BP_5

Neural crest cell migration

5

1.2E-3

GOTERM_BP_5

Steroid metabolism

14

1.5E-3

KEGG_PATHWAY

Focal adhesion

25

1.5E-3

KEGG_PATHWAY

TGF-β signaling pathway

14

1.7E-3

GOTERM_BP_5

Exocrine system development

4

1.8E-3

GOTERM_BP_5

Salivary gland morphogenesis

4

1.8E-3

GOTERM_BP_5

Salivary gland development

4

1.8E-3

GOTERM_BP_5

Negative regulation of cell differentiation

6

2.0E-3

KEGG_PATHWAY

ECM-receptor interaction

14

2.1E-3

GOTERM_BP_5

Biomineral formation

7

2.1E-3

GOTERM_BP_5

Ureteric bud branching

5

2.2E-3

GOTERM_CC_5

Intracellular

183

2.3E-3

GOTERM_BP_5

Negative regulation of signal transduction

10

2.3E-3

GOTERM_MF_5

Heparin binding

8

2.4E-3

GOTERM_BP_5

Ureteric bud development

6

2.5E-3

GOTERM_BP_5

Lung development

7

2.9E-3

GOTERM_BP_5

Gland development

4

2.9E-3

GOTERM_BP_5

Mesenchymal cell differentiation

5

2.9E-3

GOTERM_BP_5

Mesenchymal cell development

5

2.9E-3

KEGG_PATHWAY

Hedgehog signaling pathway

10

3.4E-3

GOTERM_BP_5

Embryonic appendage morphogenesis

6

3.5E-3

GOTERM_BP_5

Embryonic development (sensu Metazoa)

10

3.6E-3

GOTERM_BP_5

Bone remodeling

7

4.9E-3

GOTERM_BP_5

Alcohol biosynthesis

6

4.9E-3

GOTERM_BP_5

Negative regulation of development

6

4.9E-3

GOTERM_MF_5

Nucleic acid binding

8

5.4E-3

GOTERM_CC_5

Transcription factor complex

28

5.4E-3

KEGG_PATHWAY

Glycolysis/gluconeogenesis

10

5.7E-3

GOTERM_BP_5

Neural crest cell differentiation

4

5.8E-3

GOTERM_BP_5

Cartilage development

4

5.8E-3

GOTERM_BP_5

Cartilage condensation

4

5.8E-3

GOTERM_BP_5

Axonogenesis

8

5.9E-3

GOTERM_BP_5

Tissue remodeling

7

6.2E-3

GOTERM_BP_5

Regulation of cell migration

7

6.2E-3

GOTERM_BP_5

Neurite morphogenesis

8

6.5E-3

GOTERM_BP_5

Sterol metabolism

8

6.5E-3

GOTERM_BP_5

Cellular morphogenesis

14

7.0E-3

GOTERM_BP_5

Regulation of physiological process

28

7.0E-3

GOTERM_BP_5

Positive regulation of cellular metabolism

18

7.5E-3

GOTERM_BP_5

Regulation of cell motility

7

7.7E-3

GOTERM_BP_5

Hindlimb morphogenesis

4

7.7E-3

GOTERM_BP_5

Carboxylic acid metabolism

27

8.0E-3

GOTERM_BP_5

Carbohydrate biosynthesis

9

8.1E-3

GOTERM_BP_5

Somitogenesis

5

8.1E-3

GOTERM_BP_5

Hemopoiesis

7

8.6E-3

GOTERM_BP_5

Hemopoietic or lymphoid organ development

7

9.5E-3

GOTERM_BP_5

Regulation of cellular physiological process

24

9.6E-3

GOTERM_BP_5

Neuron development

8

1.0E-2

GOTERM_BP_5

Respiratory tube development

6

1.1E-2

GOTERM_BP_5

Embryonic pattern specification

5

1.1E-2

GOTERM_BP_5

Metanephros development

6

1.2E-2

GOTERM_BP_5

Cellular lipid metabolism

26

1.3E-2

GOTERM_BP_5

Anterior/posterior pattern formation

5

1.3E-2

GOTERM_BP_5

Protein complex assembly

11

1.5E-2

KEGG_PATHWAY

Pentose phosphate pathway

6

1.5E-2

GOTERM_CC_5

Organelle

179

1.5E-2

GOTERM_CC_5

Intracellular organelle

179

1.5E-2

GOTERM_BP_5

Glial cell differentiation

4

1.6E-2

GOTERM_BP_5

Wnt receptor signaling pathway

10

1.6E-2

GOTERM_CC_5

Membrane-bound organelle

157

1.8E-2

GOTERM_CC_5

Intracellular membrane-bound organelle

157

1.8E-2

GOTERM_MF_5

Catalytic activity

63

1.9E-2

BIOCARTA

Pertussis toxin-insensitive CCR5 signaling in macrophage

5

2.0E-2

GOTERM_BP_5

Genitalia morphogenesis

3

2.1E-2

GOTERM_BP_5

Placenta development

3

2.1E-2

GOTERM_CC_5

Nucleoplasm

31

2.1E-2

GOTERM_MF_5

Iron ion binding

16

2.1E-2

GOTERM_BP_5

Positive regulation of biological process

12

2.1E-2

GOTERM_BP_5

Odontogenesis

4

2.3E-2

GOTERM_BP_5

Positive regulation of cell proliferation

10

2.4E-2

KEGG_PATHWAY

Axon guidance

15

2.5E-2

GOTERM_BP_5

Positive regulation of cellular process

10

2.7E-2

GOTERM_BP_5

Embryonic placenta development

3

2.8E-2

GOTERM_BP_5

Cell proliferation

11

2.8E-2

GOTERM_BP_5

Negative regulation of cellular process

11

3.0E-2

GOTERM_BP_5

Inner ear morphogenesis

5

3.1E-2

GOTERM_BP_5

Negative regulation of biological process

12

3.2E-2

GOTERM_BP_5

Base-excision repair

4

3.6E-2

GOTERM_BP_5

Negative regulation of neuron differentiation

3

3.7E-2

GOTERM_MF_5

DNA N-glycosylase activity

3

3.7E-2

KEGG_PATHWAY

Fructose and mannose metabolism

8

3.8E-2

GOTERM_BP_5

Amino acid derivative metabolism

7

3.8E-2

GOTERM_CC_5

Nucleosome

7

4.1E-2

GOTERM_BP_5

Positive regulation of cellular physiological process

7

4.1E-2

GOTERM_CC_5

Chromosome

19

4.1E-2

GOTERM_MF_5

Oxidoreductase activity

11

4.2E-2

GOTERM_BP_5

Morphogenesis of an epithelium

5

4.2E-2

GOTERM_MF_5

Protein kinase activity

27

4.6E-2

GOTERM_CC_5

Nuclear lumen

35

4.6E-2

GOTERM_BP_5

Hormone metabolism

4

4.7E-2

GOTERM_MF_5

Pyrophosphatase activity

21

4.8E-2

GOTERM_CC_5

Plasma membrane

17

5.0E-2

GOTERM_BP_5

Regulation of progression through cell cycle

20

5.0E-2

GOTERM_BP_5

Odontogenesis (sensu Vertebrata)

4

5.3E-2

GOTERM_CC_5

Membrane-bound vesicle

8

5.3E-2

GOTERM_CC_5

Vesicle

8

5.3E-2

GOTERM_CC_5

Cytoplasmic vesicle

8

5.3E-2

KEGG_PATHWAY

WNT signaling pathway

15

5.5E-2

GOTERM_CC_5

Protein complex

36

5.5E-2

GOTERM_BP_5

Nucleoside metabolism

4

5.9E-2

GOTERM_BP_5

Segmentation

4

5.9E-2

GOTERM_BP_5

Morphogenesis of embryonic epithelium

4

5.9E-2

GOTERM_BP_5

Sex differentiation

5

6.0E-2

GOTERM_MF_5

Interleukin-11 receptor activity

2

6.1E-2

GOTERM_MF_5

Interleukin-11 binding

2

6.1E-2

GOTERM_CC_5

Chromatin

11

6.2E-2

GOTERM_CC_5

Heterotrimeric G-protein complex

5

6.3E-2

BIOCARTA

Sonic hedgehog (shh) pathway

4

6.4E-2

GOTERM_CC_5

Cytosol

6

6.5E-2

GOTERM_BP_5

Regulation of enzyme activity

4

6.5E-2

GOTERM_CC_5

Intrinsic to Golgi membrane

4

6.6E-2

KEGG_PATHWAY

Biosynthesis of steroids

4

6.8E-2

KEGG_PATHWAY

Huntington's disease

5

6.8E-2

GOTERM_BP_5

Eye development

5

7.0E-2

GOTERM_BP_5

Regulation of cell proliferation

9

7.2E-2

GOTERM_BP_5

Biopolymer modification

59

7.2E-2

GOTERM_BP_5

Physiological process

117

7.2E-2

GOTERM_BP_5

Cellular physiological process

100

7.7E-2

GOTERM_BP_5

Astrocyte differentiation

2

7.7E-2

GOTERM_BP_5

Regulation of astrocyte differentiation

2

7.7E-2

GOTERM_BP_5

Mesoderm morphogenesis

3

7.8E-2

GOTERM_BP_5

Mesoderm formation

3

7.8E-2

GOTERM_BP_5

Mesoderm development

3

7.8E-2

GOTERM_BP_5

T cell activation

3

7.8E-2

GOTERM_BP_5

Embryonic heart tube development

3

7.8E-2

GOTERM_BP_5

Negative regulation of Wnt receptor signaling pathway

3

7.8E-2

GOTERM_BP_5

Negative regulation of BMP signaling pathway

3

7.8E-2

GOTERM_BP_5

M phase of mitotic cell cycle

9

7.8E-2

GOTERM_BP_5

Regulation of signal transduction

8

7.8E-2

GOTERM_BP_5

Neural plate morphogenesis

4

7.9E-2

GOTERM_BP_5

Ear morphogenesis

4

7.9E-2

GOTERM_BP_5

Ear development

4

7.9E-2

KEGG_PATHWAY

Synthesis and degradation of ketone bodies

3

8.0E-2

GOTERM_BP_5

Eye development (sensu Mammalia)

5

8.6E-2

GOTERM_MF_5

Acyltransferase activity

9

8.7E-2

BIOCARTA

Repression of pain sensation by the transcriptional regulator DREAM

3

8.7E-2

BIOCARTA

IL12 and Stat4 dependent signaling pathway in Th1 development

4

8.8E-2

GOTERM_BP_5

Anatomical structure formation

3

9.0E-2

GOTERM_BP_5

Formation of primary germ layer

3

9.0E-2

GOTERM_MF_5

Bisphosphoglycerate mutase activity

2

9.0E-2

GOTERM_MF_5

Phosphoglycerate mutase activity

2

9.0E-2

GOTERM_BP_5

Phosphate metabolism

35

9.6E-2

BIOCARTA

Rho-selective guanine exchange factor akap13 mediates stress fiber formation

3

9.7E-2

KEGG_PATHWAY

Pyruvate metabolism

6

9.8E-2

KEGG_PATHWAY

Regulation regulation of actin cytoskeleton

18

9.9E-2


*Fold change >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

Open Data