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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.