Table 2

Functional annotations enriched among transcripts that are downregulated in α-MHC positive cells

Category

Term

Count

P value

GOTERM_BP_5

DNA metabolism

76

3.17 × e^-24

GOTERM_BP_5

M phase

41

1.79 × e^-23

GOTERM_BP_5

DNA replication

35

2.91 × e^-19

GOTERM_BP_5

Mitotic cell cycle

35

1.92 × e^-17

KEGG_PATHWAY

Cell cycle

32

7.70 × e^-17

GOTERM_MF_5

ATP binding

101

3.13 × e^-15

GOTERM_CC_5

Chromosome

46

9.39 × e^-13

GOTERM_BP_5

DNA repair

27

2.88 × e^-10

GOTERM_BP_5

Regulation of cell cycle

40

7.18 × e^-10

GOTERM_CC_5

Chromosome, pericentric region

15

2.39 × e^-09

GOTERM_BP_5

RNA processing

32

5.21 × e^-09

GOTERM_BP_5

mRNA metabolism

24

1.28 × e^-08

GOTERM_BP_5

RNA metabolism

37

1.29 × e^-08

GOTERM_CC_5

Nucleus

229

2.04 × e^-07

GOTERM_MF_5

Exonuclease activity

12

9.96 × e^-07

GOTERM_CC_5

Kinetochore

9

1.68 × e^-06

GOTERM_CC_5

Replication fork

9

1.68 × e^-06

GOTERM_CC_5

Condensed chromosome

12

3.78 × e^-06

GOTERM_CC_5

Replisome

8

8.86 × e^-06

GOTERM_MF_5

Pyrophosphatase activity

40

1.85 × e^-05

GOTERM_BP_5

Regulation of DNA metabolism

6

4.69 × e^-05

KEGG_PATHWAY

Pyrimidine metabolism

14

4.94 × e^-05

GOTERM_CC_5

Spindle

13

8.62 × e^-05

GOTERM_BP_5

DNA recombination

11

1.44 × e^-04

GOTERM_BP_5

DNA damage response, signal transduction

6

3.13 × e^-04

GOTERM_BP_5

Coenzyme metabolism

15

8.57 × e^-04

GOTERM_BP_5

Carboxylic acid metabolism

27

1.04 × e^-03

GOTERM_BP_5

Nuclear transport

11

1.07 × e^-03

GOTERM_CC_5

Nucleolus

16

1.22 × e^-03

GOTERM_BP_5

Amine biosynthesis

9

1.23 × e^-03

GOTERM_BP_5

Amino acid metabolism

16

2.25 × e^-03

GOTERM_CC_5

Microtubule cytoskeleton

24

3.62 × e^-03

GOTERM_BP_5

Folic acid and derivative metabolism

4

3.75 × e^-03

GOTERM_BP_5

Nucleocytoplasmic transport

11

4.02 × e^-03

GOTERM_BP_5

Cellular protein metabolism

135

4.25 × e^-03

GOTERM_BP_5

Cytoskeleton organization and biogenesis

28

5.66 × e^-03

KEGG_PATHWAY

Purine metabolism

14

6.33 × e^-03

KEGG_PATHWAY

Glycine, serine and threonine metabolism

7

1.01 × e^-02

KEGG_PATHWAY

DNA polymerase

6

1.10 × e^-02

GOTERM_BP_5

Dna packaging

15

1.16 × e^-02

GOTERM_CC_5

Nuclear chromosome

8

1.17 × e^-02

GOTERM_CC_5

Spindle pole

8

1.17 × e^-02

GOTERM_MF_5

S-adenosylmethionine-dependent methyltransferase activity

9

1.24 × e^-02

BIOCARTA

Cell cycle: G2/M checkpoint

7

1.33 × e^-02

GOTERM_BP_5

Chromosome organization and biogenesis

19

1.36 × e^-02

BIOCARTA

Cell cycle: G1/S check point

7

1.59 × e^-02

GOTERM_CC_5

Delta DNA polymerase complex

3

1.59 × e^-02

BIOCARTA

Role of Ran in mitotic spindle regulation

5

1.60 × e^-02

GOTERM_BP_5

DNA modification

6

1.64 × e^-02

GOTERM_BP_5

Phosphate metabolism

43

1.65 × e^-02

GOTERM_BP_5

Determination of left/right symmetry

4

1.72 × e^-02

GOTERM_BP_5

Sulfur amino acid metabolism

4

1.72 × e^-02

GOTERM_BP_5

Ribosome biogenesis and assembly

9

1.87 × e^-02

BIOCARTA

Role of BRCA1

6

1.89 × e^-02

GOTERM_BP_5

Response to radiation

6

1.99 × e^-02

KEGG_PATHWAY

Methionine metabolism

4

2.03 × e^-02

BIOCARTA

CDK regulation of DNA replication

4

2.15 × e^-02

BIOCARTA

RB tumor suppressor/checkpoint signaling in response to DNA damage

4

2.15 × e^-02

GOTERM_BP_5

Cellular carbohydrate metabolism

16

2.21 × e^-02

GOTERM_BP_5

rRNA metabolism

5

2.50 × e^-02

GOTERM_BP_5

Nucleic acid transport

5

2.78 × e^-02

GOTERM_BP_5

RNA transport

5

2.78 × e^-02

GOTERM_CC_5

Centrosome

6

2.94 × e^-02

BIOCARTA

E2F1 destruction pathway

4

2.96 × e^-02

BIOCARTA

Sonic Hedgehog (SHH) receptor Ptc1 regulates cell cycle

4

2.96 × e^-02

GOTERM_MF_5

Amino acid permease activity

3

3.17 × e^-02

KEGG_PATHWAY

One carbon pool by folate

4

3.24 × e^-02

GOTERM_CC_5

Nuclear pore

6

3.30 × e^-02

GOTERM_BP_5

Heparan sulfate proteoglycan metabolism

3

3.40 × e^-02

GOTERM_BP_5

Nucleotide metabolism

13

3.93 × e^-02

GOTERM_MF_5

Glycine hydroxymethyltransferase activity

3

3.97 × e^-02

GOTERM_MF_5

Protein kinase activity

32

4.12 × e^-02

GOTERM_BP_5

Nucleobase, nucleoside, nucleotide and nucleic acid transport

5

4.51 × e^-02

GOTERM_BP_5

Positive regulation of programmed cell death

10

4.61 × e^-02

GOTERM_MF_5

DNA-directed DNA polymerase activity

4

4.87 × e^-02

BIOCARTA

Activation of Src by protein-tyrosine phosphatase alpha

3

5.41 × e^-02

BIOCARTA

Cyclins and cell cycle regulation

6

5.41 × e^-02

GOTERM_BP_5

Steroid metabolism

9

5.54 × e^-02

GOTERM_MF_5

Pre-mRNA splicing factor activity

5

6.43 × e^-02

GOTERM_MF_5

Methylene-tetrahydrofolate dehydrogenase activity

2

7.11 × e^-02

GOTERM_BP_5

Regulation of cell migration

5

7.20 × e^-02

BIOCARTA

Cdc25 and chk1 regulatory pathway in response to DNA damage

3

7.55 × e^-02

GOTERM_CC_5

Chromatin

13

8.01 × e^-02

GOTERM_BP_5

Regulation of apoptosis

16

8.13 × e^-02

GOTERM_CC_5

Nuclear membrane

9

8.33 × e^-02

GOTERM_BP_5

Nucleotide biosynthesis

9

8.59 × e^-02

GOTERM_CC_5

Nuclear body

4

8.81 × e^-02

GOTERM_BP_5

Regulation of programmed cell death

16

8.95 × e^-02

KEGG_PATHWAY

Urea cycle and metabolism of amino groups

4

9.73 × e^-02

BIOCARTA

Regulation of p27 phosphorylation during cell cycle progression

4

9.84 × e^-02

GOTERM_CC_5

Heterochromatin

4

9.89 × e^-02

Functional annotations that are enriched among transcripts downregulated in myosin heavy chain (MHC) positive cells (intersection of down-regulation in the 15-day-old α-MHC⁺ cardiomyocytes [twofold, Student's t-test P value < 0.01] compared with the control cells in the 15-day-old embryoid bodies and compared with the undifferentiated α-MHC embryonic stem cells). 'Count' refers to the number of transcripts in the respective category; the 'P value' column shows the value of Fisher's exact t-test, as used by DAVID to measure the enrichment in annotation terms. GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MAPK, mitogen-activated protein kinase

Doss et al. Genome Biology 2007 8:R56   doi:10.1186/gb-2007-8-4-r56