. 2006 Oct 25;26(43):11083–11110. doi: 10.1523/JNEUROSCI.2766-06.2006

Table 3.

Significant GO terms according to a Z score >1.96 (which corresponds to a p value of 0.05) according to the lists of ontology classes (processes, functions, and components) at 1 d (D), the latent period (W), or in the chronic phase (M) in CA3 and EC

GOID			No. genes up	% changed	Z score
Group D		726 probes upregulated in both CA3 and EC (406 GO)
		Process
6357		Regulation of transcription from RNA polymerase II promoter	3	60	4.73
6986		Response to unfolded protein	6	60	4.47
45944		Positive regulation of transcription from RNA polymerase II promoter	3	38	4.15
6950	M	Response to stress	3	50	4.08
6412		Protein biosynthesis	17	29	3.79
6413		Translational initiation	5	42	3.51
6355		Regulation of transcription, DNA-dependent	32	19	3.31
6953	M	Acute-phase response	4	50	3.15
6915	W	Apoptosis	8	24	3.02
6886	M	Intracellular protein transport	15	19	2.82
6260		DNA replication	6	33	2.75
6955	WM	Immune response	8	28	2.67
6350		Transcription	20	21	2.59
6457	M	Protein folding	15	26	2.57
6888	M	ER to Golgi transport	6	32	2.45
42981	W	Regulation of apoptosis	7	37	2.31
8152		Metabolism	5	5	2.20
30163		Protein catabolism	3	33	2.10
7517		Muscle development	3	21	2.05
		Function
8243		Plasminogen activator activity	3	100	4.52
16563		Transcriptional activator activity	9	45	4.51
3743		Translation initiation factor activity	11	42	4.51
3676		Nucleic acid binding	18	14	3.93
17017		MAP kinase phosphatase activity	3	75	3.72
5544		Calcium-dependent phospholipid binding	4	50	3.15
3690	W	Double-stranded DNA binding	4	50	3.15
51082		Unfolded protein binding	11	28	2.89
4298		Threonine endopeptidase activity	4	40	2.57
3723		RNA binding	14	25	2.54
3677		DNA binding	20	16	2.48
31072	M	Heat shock protein binding	5	33	2.38
3700		Transcription factor activity	17	21	2.28
		Component
5634		Nucleus	82	19	3.88
5622		Intracellular	12	15	2.78
5839		Proteasome core complex (sensu Eukaryota)	4	40	2.57
9986	M	Cell surface	3	33	2.34
5615	W	Extracellular space	10	23	2.19

Group W		559 probes upregulated in both CA3 and EC (298 GO)
		Process
6955	DM	Immune response	13	45	8.65
19886		Antigen processing, exogenous antigen via MHC class II	6	100	7.61
19884		Antigen presentation, exogenous antigen	5	100	6.94
9611		Response to wounding	4	67	4.82
6954		Inflammatory response	5	42	4.50
8283		Cell proliferation	4	33	4.25
7242	M	Intracellular signaling cascade	18	20	3.74
6508		Proteolysis	19	19	3.43
6935		Chemotaxis	3	43	3.32
7165		Signal transduction	15	12	3.04
6915	D	Apoptosis	4	12	2.56
6631		Fatty acid metabolism	5	22	2.53
42981	D	Regulation of apoptosis	4	21	2.51
6817	M	Phosphate transport	4	27	2.29
30154		Cell differentiation	4	9	2.07
		Function
3690		MHC class II receptor activity	5	100	6.94
30106	DM	Double-stranded DNA binding	4	50	3.94
8233		MHC class I receptor activity	3	20	3.88
4871		Peptidase activity	6	14	3.57
16798		Signal transducer activity	5	31	3.15
4872	M	Hydrolase activity, acting on glycosyl bonds	4	13	2.95
16787		Receptor activity	23	10	2.92
16798		Signal transducer activity	5	31	3.15
4872	M	Hydrolase activity, acting on glycosyl bonds	4	13	2.95
16787		Receptor activity	23	10	2.92
5096		Hydrolase activity	17	25	2.54
4896		GTPase activator activity	3	100	2.29
		Component
5764	M	Lysosome	16	67	10.23
16020		Membrane	55	12	3.02
5737	M	Cytoplasm	15	13	2.50
5615	D	Extracellular space	8	18	2.30
5886	M	Plasma membrane	4	11	2.02
	M	609 probes upregulated in CA3 (307 GO)
		Process
6817	W	Phosphate transport	6	40	3.98
6953	D	Acute-phase response	3	38	2.66
7242	W	Intracellular signaling cascade	11	15	2.55
6888	D	ER to Golgi transport	5	26	2.46
7264		Small GTPase mediated signal transduction	13	18	2.42
6886	D	Intracellular protein transport	13	16	2.36
6950	D	Response to stress	3	15	2.31
7155		Cell adhesion	7	18	2.24
6955	DW	Immune response	3	18	2.24
16567		Protein ubiquitination	11	17	2.10
		Function
3690	D	Double-stranded DNA binding	3	38	2.66
31072	D	Heat shock protein binding	4	27	2.23
16874		Ligase activity	5	17	2.12
4842		Ubiquitin-protein ligase activity	12	17	2.08

Group M		369 probes upregulated in EC (200 GO)
		Process
15986		ATP synthesis coupled proton transport	4	24	2.93
7218		Neuropeptide signaling pathway	3	21	2.33
9058		Biosynthesis	4	33	2.32
5975		Carbohydrate metabolism	5	12	2.22
6865		Amino acid transport	3	23	2.18
6457	D	Protein folding	8	14	2.05
		Function
5544	D	Calcium-dependent phospholipid binding	4	50	5.08
46933		Hydrogen-transporting ATP synthase activity, rotational mechanism	4	25	3.08
46961		Hydrogen-transporting ATPase activity, rotational mechanism	4	25	3.08
16798		Hydrolase activity, acting on glycosyl bonds	3	23	2.62
31072	D	Heat shock protein binding	3	20	2.18
		Component
5764	W	Lysosome	6	25	4.21
9986	D	Cell surface	3	33	4.10
16469		Proton-transporting two-sector ATPase complex	4	25	2.93
5737	W	Cytoplasm	13	11	2.69
5886	W	Plasma membrane	3	9	2.19
		Process
15986		ATP synthesis coupled proton transport	4	24	2.93
7218		Neuropeptide signaling pathway	3	21	2.33
9058		Biosynthesis	4	33	2.32
5975		Carbohydrate metabolism	5	12	2.22
6865		Amino acid transport	3	23	2.18
6457	D	Protein folding	8	14	2.05
		Function
5544	D	Calcium-dependent phospholipid binding	4	50	5.08
46933		Hydrogen-transporting ATP synthase activity, rotational mechanism	4	25	3.08
46961		Hydrogen-transporting ATPase activity, rotational mechanism	4	25	3.08
16798		Hydrolase activity, acting on glycosyl bonds	3	23	2.62
31072	D	Heat shock protein binding	3	20	2.18
		Component
5764	W	Lysosome	6	25	4.21
9986	D	Cell surface	3	33	4.10
16469		Proton-transporting two-sector ATPase complex	4	25	2.93
5737	W	Cytoplasm	13	11	2.69
5886	W	Plasma membrane	3	9	2.19

Group D		763 probes downregulated in both CA3 and EC (317 GO)
		Process
7268		Synaptic transmission	4	24	4.65
48167		Regulation of synaptic plasticity	3	50	3.92
7417		CNS development	3	60	2.92
6874		Calcium ion homeostasis	3	75	2.90
6816	W	Calcium ion transport	6	29	2.84
7399		Nervous system development	5	22	2.77
8654		Phospholipid biosynthesis	3	38	2.50
6811		Ion transport	15	18	2.20
7155		Cell adhesion	8	19	2.12
6468	W	Protein amino acid phosphorylation	21	15	1.98
		Function
4685	WM	Calcium- and calmodulin-dependent protein kinase activity	5	100	6.71
4364		Glutathione transferase activity	3	60	3.73
30170		Pyridoxal phosphate binding	3	60	3.73
5516	W	Calmodulin binding	9	29	3.55
5262		Calcium channel activity	3	33	2.84
16740		Transferase activity	35	16	2.83
3779	W	Actin binding	10	23	2.75
5230		Extracellular ligand-gated ion channel activity	3	30	2.71
5216	W	Ion channel activity	8	22	2.70
3774		Motor activity	5	31	2.55
16301		Kinase activity	9	17	2.37
4890		GABA_A receptor activity	3	33	2.33
19992		Diacylglycerol binding	4	29	2.32
5509		Calcium ion binding	26	15	2.23
4674	W	Protein serine/threonine kinase activity	16	16	2.22
5215		Transporter activity	14	17	2.19
5515	W	Protein binding	30	12	2.17
3924	W	GTPase activity	4	27	2.15
5234		Glutamate-gated ion channel activity	3	30	2.11
15297		Antiporter activity	3	43	2.11
16757		Transferase activity, transferring glycosyl groups	5	23	1.96
		Component
5954		Calcium- and calmodulin-dependent protein kinase complex	3	100	5.19
5887		Integral to plasma membrane	4	21	2.80
5886	W	Plasma membrane	6	17	2.59
8021		Synaptic vesicle	3	23	2.52
16020	W	Membrane	61	14	2.48
45211	M	Postsynaptic membrane	6	24	2.34
16021	M	Integral to membrane	71	12	2.19

Group W		325 probes downregulated in both CA3 and EC (147 GO)
		Process
46928		Regulation of neurotransmitter secretion	3	75	6.69
6695		Cholesterol biosynthesis	4	40	6.44
6836		Neurotransmitter transport	4	22	3.41
6629		Lipid metabolism	3	7	2.66
6468	D	Protein amino acid phosphorylation	13	9	2.64
6816	D	Calcium ion transport	3	14	2.11
		Function
4685	D	Calcium- and calmodulin-dependent protein kinase activity	3	60	5.89
5516	D	Calmodulin binding	6	19	3.91
4674	D	Protein serine/threonine kinase activity	11	11	3.14
19992	D	Diacylglycerol binding	3	21	2.99
3924	D	GTPase activity	3	20	2.83
5216	D	Ion channel activity	3	8	2.34
20037		Heme binding	3	14	2.11
5515	D	Protein binding	13	5	2.10
3779	D	Actin binding	5	11	2.08
		Component
8076		Voltage-gated potassium channel complex	4	20	3.27
5886	D	Plasma membrane	4	11	2.67
16020	D	Membrane	33	7	2.67
5856		Cytoskeleton	6	13	2.38

Group M		627 probes downregulated in CA3 (279 GO)
		Function
4685		Calcium- and calmodulin-dependent protein kinase activity	3	60	4.04
3899		DNA-directed RNA polymerase activity	4	44	3.78
3735		Structural constituent of ribosome	9	24	3.35
5198		Structural molecule activity	4	11	2.44
		Component
5840		Ribosome	7	23	3.04
45211	W	Postsynaptic membrane	5	20	1.98

Group M		313 probes downregulated in EC (110 GO)
		Process
6814		Sodium ion transport	3	15	2.82
		Function
5516	DW	Calmodulin binding	5	16	3.87
		Component
45211	W	Postsynaptic membrane	3	12	2.34

The total number of genes upregulated or downregulated at a specific stage is indicated at the top; the number of GO-related terms is in parentheses. In the first column, the GO identity is shown; the second column indicates whether a process also occurred during another epileptogenic stage. The fourth column shows the number of genes that are upregulated or downregulated (“local term”); the fifth column shows the percentage of the genes in the specific GO term that is upregulated or downregulated; the sixth column indicates the Z score.