Molecular Patterns of Neurodevelopmental Preconditioning: A Study of the Effects of Antenatal Steroid Therapy in a Protein-Restriction Mouse Model

Table 2

Ontological review of biologic processes.

(a) Comparison of gene ontology slim terms of biological processes involved for the total number of genes on the microarray as compared to the combined significantly regulated genes and the genes uniquely regulated per treatment

Biological process	Gene count (frequency)
	Total number of genes†	Significant genes‡	C-D/S only	PR-D/S only	C-S only	PR-S only
Cell adhesion	460 (0.04202)	21 (0.06325301)	0 (0.00000)	5 (0.08621)§	0 (0.00000)	3 (0.06818)§
Cell-cell signaling	403 (0.03682)	22 (0.06626506)	2 (0.11765)	5 (0.08621)	2 (0.15385)	0 (0.00000)
Cell cycle and proliferation	1329 (0.12141)	35 (0.10542169)	0 (0.00000)	6 (0.10345)	2 (0.15385)	0 (0.00000)
Death	946 (0.08642)	29 (0.08734940)	2 (0.11765)	5 (0.08621)	0 (0.00000)	2 (0.04545)
Cell organization and biogenesis	2327 (0.21259)	96 (0.28915663)	6 (0.35294)	14 (0.24138)	4 (0.30769)	11 (0.25000)
Protein metabolism	2199 (0.20090)	61 (0.18373494)	3 (0.17647)	13 (0.22414)	2 (0.15385)	7 (0.15909)
DNA metabolism	438 (0.04001)	20 (0.06024096)	0 (0.00000)	2 (0.03448)¶	0 (0.00000)	0 (0.00000)
RNA metabolism	2020 (0.18454)	65 (0.19578313)	7 (0.41176)	14 (0.24138)	3 (0.23077)	7 (0.15909)
Other metabolic processes	1657 (0.15138)	57 (0.17168675)	4 (0.23529)	10 (0.17241)	2 (0.15385)	9 (0.20455)
Stress response	1156 (0.10561)	29 (0.08734940)	2 (0.11765)ß	6 (0.10345)ß	0 (0.00000)	0 (0.00000)
Transport	1929 (0.17623)	72 (0.21686747)	4 (0.23529)	13 (0.22414)	4 (0.30769)	5 (0.11364)
Developmental processes	2000 (0.18272)	83 (0.25000000)	5 (0.29412)	13 (0.22414)	5 (0.38462)	10 (0.22727)
Signal transduction	2111 (0.19286)	59 (0.17771084)	0 (0.00000)	10 (0.17241)	2 (0.15385)	3 (0.06818)
Unknown biological; processes	0 (0.00000)	0 (0.00000000)	0 (0.00000)	0 (0.00000)	0 (0.00000)	0 (0.00000)
Other biological processes	10946 (1.00000)	331 (0.99698795)	16 (0.94118)	57 (0.98276)	12 (0.92308)	43 (0.97727)
All biological processes	10946 (1.00000)	332 (1.00000000)	17 (1.00000)	58 (1.00000)	13 (1.00000)	44 (1.00000)

†Only genes without any absent calls were included in the analysis from 23,522 transcripts on the microarray.
‡Genes determined by up or down regulation within the 1.5 fold change threshold.
§Cell adhesion genes: PR-D/S only (Col1a1, Atp1b2, Ctnnd1, Rpsa, and Fat4); PR-S only (Cdh2, Edil3, and Astn1).
¶DNA metabolism: PR-D/S only (Tcf3, Mapk8).
ßStress response genes: C-D/S only (Brsk1, Rarres2); PR-D/S only (Klk8, Myo6, Ndufa6, Col1a1, Mapk8, and Phlda3).

(b) Top 25 biological processes among the significantly regulated genes based on 𝑃 values

GO ID	GO term	Frequency	Genome frequency	𝑃 value	Corrected 𝑃 value
GO:0009987	Cellular process	0.68072	0.39346	2.0856𝐸−26	2.6196𝐸−23
GO:0071841	Cellular component organization or biogenesis at cellular level	0.27108	0.08456	8.0847𝐸−24	1.0154𝐸−20
GO:0071842	Cellular component organization at cellular level	0.25904	0.08100	1.2822𝐸−22	1.6105𝐸−19
GO:0071840	Cellular component organization or biogenesis	0.30120	0.10864	6.0965𝐸−22	7.6573𝐸−19
GO:0016043	Cellular component organization	0.28916	0.10476	7.5917𝐸−21	9.5351𝐸−18
GO:0008152	Metabolic process	0.50301	0.26565	1.9862𝐸−20	2.4947𝐸−17
GO:0044237	Cellular metabolic process	0.45181	0.22384	2.2263𝐸−20	2.7962𝐸−17
GO:0044238	Primary metabolic process	0.43976	0.22525	2.6340𝐸−18	3.3082𝐸−15
GO:0007399	Nervous system development	0.15060	0.04143	2.9821𝐸−15	3.7455𝐸−12
GO:0043170	Macromolecule metabolic process	0.37048	0.18900	5.7101𝐸−15	7.1719𝐸−12
GO:0051179	Localization	0.26807	0.11543	1.3853𝐸−14	1.7399𝐸−11
GO:0048699	Generation of neurons	0.11747	0.02708	1.8462𝐸−14	2.3188𝐸−11
GO:0030182	Neuron differentiation	0.11145	0.02443	1.9738𝐸−14	2.4790𝐸−11
GO:0044260	Cellular macromolecule metabolic process	0.33434	0.16512	2.9036𝐸−14	3.6469𝐸−11
GO:0022008	Neurogenesis	0.12048	0.02896	3.2387𝐸−14	4.0678𝐸−11
GO:0007275	Multicellular organismal development	0.25000	0.10479	3.3420𝐸−14	4.1975𝐸−11
GO:0006996	Organelle organization	0.16867	0.05448	4.7022𝐸−14	5.9060𝐸−11
GO:0048666	Neuron development	0.09639	0.01882	5.6471𝐸−14	7.0927𝐸−11
GO:0065007	Biological regulation	0.45783	0.27182	2.5651𝐸−13	3.2218𝐸−10
GO:0034641	Cellular nitrogen compound metabolic process	0.28614	0.13631	5.9844𝐸−13	7.5165𝐸−10
GO:0009058	Biosynthetic process	0.27108	0.12543	6.0854𝐸−13	7.6433𝐸−10
GO:0032502	Developmental process	0.25904	0.11705	6.6540𝐸−13	8.3574𝐸−10
GO:0006807	Nitrogen compound metabolic process	0.28916	0.13916	7.8812𝐸−13	9.8988𝐸−10
GO:0006139	Nucleobase, nucleoside, nucleotide, and nucleic acid metabolic process	0.27108	0.12602	7.9334𝐸−13	9.9643𝐸−10
GO:0031175	Neuron projection development	0.08434	0.01588	9.5266𝐸−13	1.1965𝐸−09