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Table 2 Gene ontology analysis.

From: Epidermal growth factor (EGF) withdrawal masks gene expression differences in the study of pituitary adenylate cyclase-activating polypeptide (PACAP) activation of primary neural stem cell proliferation

Biological process enriched in neurosphere (NS) control sample

No of DE genes in all treatments

No of genes on array

Fisher Exact

mitotic cell cycle

35

136

3.840E-22

DNA replication and chromosome cycle

24

72

3.320E-18

cell cycle

43

307

2.360E-16

cell proliferation

46

362

7.620E-16

DNA replication

20

61

3.770E-15

S phase of mitotic cell cycle

20

62

5.400E-15

DNA-dependent DNA replication

11

24

1.160E-10

DNA metabolism

29

218

1.830E-10

DNA replication initiation

7

8

4.430E-10

mitosis

12

48

5.240E-08

M phase of mitotic cell cycle

12

48

5.240E-08

cell growth and/or maintenance

79

1411

2.740E-07

nuclear division

12

58

4.950E-07

M phase

12

61

8.830E-07

cellular physiological process

82

1564

2.770E-06

cytokinesis

11

63

8.760E-06

nucleosome assembly

6

21

5.920E-05

regulation of cell cycle

15

138

7.790E-05

physiological process

135

3454

6.310E-04

DNA packaging

9

80

1.750E-03

Biological process enriched in treated (PACAP. Prol Cont and Diff Cont) samples

No of DE genes in all treatments

No of genes on array

Fisher Exact

microtubule-based process

7

64

1.340E-03

development

22

456

3.400E-03

neurogenesis

8

99

4.300E-03

organogenesis

14

243

4.390E-03

morphogenesis

15

282

6.730E-03

cytoskeleton organization and biogenesis

9

134

8.430E-03

organelle organization and biogenesis

10

175

1.650E-02

cellular process

65

2144

6.560E-02

cytoplasm organization and biogenesis

10

222

6.720E-02

lipid metabolism

8

173

8.570E-02

membrane lipid metabolism

3

42

9.840E-02

cell adhesion

7

162

1.360E-01

cell communication

27

835

1.440E-01

cell organization and biogenesis

12

331

1.620E-01

regulation of biological process

5

110

1.650E-01

ion transport

7

188

2.280E-01

cellular physiological process

45

1564

2.640E-01

cation transport

5

135

2.850E-01

cell death

5

144

3.330E-01

cell surface receptor linked signal transduction

9

286

3.440E-01

  1. The most highly overrepresented gene ontology themes among the genes that were differentially expressed in all treatments. Analysis was restricted to themes of category biological process. Genes with M-value > | 0.6 | and p < 0.0001, calculated by empirical Bayes moderated t-test and a Holm adjustment for multiple testing, are included. Jacknife Fisher's exact probability test was used to identify over-represented themes in the data. Corresponding p-values are listed.