Time-series gene expression profiles in AGS cells stimulated with Helicobacter pylori

Table 4 Statistically significant changed gene ontology at each time point

Time point (h)	Up-regulation					Down-regulation
	GO ID	GO name	Genes	P value	Code	GO ID	GO name	Genes	P value	Code
0.5	GO:0008201	Heparin binding	5	7.1E-4	MF	GO:0006955	Immune response	20	0.00000	BP
	GO:0008134	Transcription factor binding	4	0.01585	MF	GO:0009615	Response to virus	10	0.00000	BP
	GO:0003700	Transcription activity	10	0.02835	MF	GO:0008150	Biological process	15	0.00896	BP
	GO:0008083	Growth factor activit	4	0.03882	MF	GO:0007267	Cell-cell signaling	10	0.00966	BP
	GO:0005576	Extracellular region	15	0.02875	CC	GO:0006935	Chemotaxis	6	0.01581	BP
	GO:0005634	Nucleus	28	0.03452	CC	GO:0006954	Inflammatory response	8	0.01581	BP
						GO:0008285	Negative regulation of cell proliferation	7	0.03430	BP
						GO:0007275	Multicellular organismal development	16	0.03576	BP
						GO:0008009	Chemokine activity	7	0.00000	MF
						GO:0046870	Cadmium ion binding	3	0.00194	MF
						GO:0016779	Nucleotidyl transferase activity	5	0.02486	MF
						GO:0005576	Extracellular region	37	0.00000	CC
						GO:0005615	Extracellular space	14	2.0E-4	CC
						GO:0005634	Nucleus	56	7.0E-4	CC
1	GO:0008201	Heparin binding	5	0.00265	MF	GO:0008009	Chemokine activity	6	3.5E-4	MF
	GO:0003700	Transcription factor activity	13	0.00886	MF	GO:0046870	Cadmium ion binding	3	0.00264	MF
	GO:0005515	Protein binding	38	0.01716	MF	GO:0003677	DNA binding	26	0.00264	MF
	GO:0045766	Positive regulation of angiogenesis	3	0.01125	BP	GO:0046872	Metal ion binding	36	0.01144	MF
	GO:0001558	Regulation of cell growth	6	0.01502	BP	GO:0008270	Zinc ion binding	34	0.02041	MF
	GO:0006915	Apoptosis	8	0.02591	BP	GO:0003674	Molecular function	15	0.02257	MF
	GO:0008285	Negative regulation of cell proliferation	6	0.02591	BP	GO:0003676	Nucleic acid binding	13	0.02257	MF
	GO:0005634	Nucleus	36	0.00597	CC	GO:0016779	Nucleotidyl transferase activity	4	0.02571	MF
	GO:0005575	Cellular component	10	0.02160	CC	GO:0005515	Protein binding	61	0.03204	MF
						GO:0003704	Specific RNA polymerase II transcription factor activity	3	0.04080	MF
						GO:0009615	Response to virus	10	0.00000	BP
						GO:0006955	Immune response	18	0.00000	BP
						GO:0006355	Regulation of transcription DNA-dependent	39	4.0E-5	BP
						GO:0006350	Transcription	31	4.5E-4	BP
						GO:0008150	Biological process	18	0.00348	BP
						GO:0007267	Cell-cell signaling	11	0.00480	BP
						GO:0006954	Inflammatory response	8	0.03385	BP
						GO:0045087	Innate immune response	5	0.04274	BP
						GO:0005634	Nucleus	71	0.00000	CC
						GO:0005576	Extracellular region	37	1.1E-4	CC
						GO:0005615	Extracellular space	13	0.00474	CC
						GO:0005622	Intracellular	31	0.01344	CC
						GO:0005575	Cellular component	15	0.03381	CC
2	GO:0003700	Transcription factor activity	18	1.4E-4	MF	GO:0009615	Response to virus	10	0.00000	BP
	GO:0008201	Heparin binding	5	0.00193	MF	GO:0006955	Immune response	16	0.00000	BP
	GO:0043565	Sequence-specific DNA binding	10	0.01819	MF	GO:0008150	Biological process	18	6.6E-4	BP
	GO:0008083	Growth factor activity	5	0.01885	MF	GO:0007267	Cell-cell signaling	10	0.01111	BP
	GO:0005178	Integrin binding	3	0.02722	MF	GO:0006954	Inflammatory response	8	0.01911	BP
	GO:0008134	Transcription factor binding	4	0.02722	MF	GO:0045087	Innate immune response	5	0.02866	BP
	GO:0008009	Chemokine activity	3	0.02849	MF	GO:0007565	Female pregnancy	5	0.03928	BP
	GO:0046872	Metal ion binding	23	0.04806	MF	GO:0005576	Extracellular region	36	1.0E-5	CC
	GO:0045944	Positive regulation of transcription from RNA polymerase II promoter	7	0.00234	BP	GO:0005615	Extracellular space	13	0.00113	CC
	GO:0006955	Immune response	10	0.00470	BP	GO:0005634	Nucleus	51	0.00899	CC
	GO:0008285	Negative regulation of cell proliferation	7	0.00681	BP	GO:0046870	Cadmium ion binding	3	0.01145	MF
	GO:0000122	Negative regulation of transcription from RNA polymerase II promoter	6	0.00681	BP	GO:0016831	Carboxy-lyase activity	3	0.02198	MF
	GO:0006915	Apoptosis	9	0.00713	BP	GO:0030674	Protein binding bridging	4	0.04373	MF
	GO:0006954	Inflammatory response	7	0.00769	BP
	GO:0001558	Regulation of cell growth	5	0.00914	BP
	GO:0009611	Response to wounding	3	0.01457	BP
	GO:0005615	Extracellular space	12	8E-5	CC
	GO:0005634	Nucleus	42	2.4E-4	CC
	GO:0005576	Extracellular region	22	4E-4	CC
	GO:0030173	Integral to Golgi membrane	3	0.02101	CC
4	GO:0008083	Growth factor activity	8	1.0E-5	MF	GO:0009615	Response to virus	12	0.00000	BP
	GO:0005125	Cytokine activity	6	3.7E-4	MF	GO:0007565	Female pregnancy	9	1.6E-4	BP
	GO:0046983	Protein dimerization activity	6	0.00123	MF	GO:0006955	Immune response	17	5.0E-4	BP
	GO:0005100	Rho GTPase activator activity	3	0.00268	MF	GO:0001525	Angiogenesis	7	0.02671	BP
	GO:0008201	Heparin binding	4	0.00826	MF	GO:0007267	Cell-cell signaling	10	0.02671	BP
	GO:0003700	Transcription factor activity	13	0.00826	MF	GO:0008150	Biological process	19	0.02928	BP
	GO:0008047	Enzyme activator activity	3	0.01045	MF	GO:0016477	Cell migration	5	0.03984	BP
	GO:0005178	Integrin binding	3	0.01447	MF	GO:0005576	Extracellular region	45	0.00000	CC
	GO:0016563	Transcription activator activity	4	0.02237	MF	GO:0005577	Fibrinogen complex	3	6.0E-4	CC
	GO:0005515	Protein binding	33	0.03960	MF	GO:0005615	Extracellular space	14	0.00843	CC
	GO:0043565	Sequence-specific DNA binding	8	0.03960	MF	GO:0031093	Platelet α granule lumen	4	0.01203	CC
	GO:0006955	Immune response	11	2.4E-4	BP	GO:0016020	Membrane	61	0.03962	CC
	GO:0006915	Apoptosis	9	0.00440	BP	GO:0005794	Golgi apparatus	15	0.03962	CC
	GO:0030183	B cell differentiation	3	0.01798	BP
	GO:0045944	Positive regulation of transcription from RNA polymerase II promoter	5	0.03323	BP
	GO:0000079	Regulation of cyclin-dependent protein kinase activity	3	0.03704	BP
	GO:0007050	Cell cycle arrest	4	0.03704	BP
	GO:0008284	Positive regulation of cell proliferation	5	0.03704	BP
	GO:0007267	Cell-cell signaling	6	0.03704	BP
	GO:0001558	Regulation of cell growth	5	0.0407	BP
6	GO:0005515	Protein binding	65	0.00000	MF	GO:0046870	Cadmium ion binding	3	0.00135	MF
	GO:0003700	Transcription factor activity	24	1.0E-5	MF	GO:0003674	Molecular function	13	0.00852	MF
	GO:0008083	Growth factor activity	8	3.5E-4	MF	GO:0008009	Chemokine activity	4	0.00852	MF
	GO:0003714	Transcription co-repressor activity	7	3.5E-4	MF	GO:0003950	NAD+ADP-ribosyl transferase activity	3	0.01169	MF
	GO:0005125	Cytokine activity	8	3.5E-4	MF	GO:0030674	Protein binding bridging	3	0.04041	MF
	GO:0005100	Rho GTPase activator activity	4	3.5E-4	MF	GO:0009615	Response to virus	12	0.00000	BP
	GO:0003700	Transcription factor activity	7	6.2E-4	MF	GO:0006955	Immune response	16	0.00000	BP
	GO:0046983	Protein dimerization activity	7	6.9E-4	MF	GO:0007565	Female pregnancy	9	0.00000	BP
	GO:0008270	Zinc ion binding	32	0.00504	MF	GO:0008150	Biological process	14	0.00612	BP
	GO:0046872	Metal ion binding	32	0.00827	MF	GO:0007267	Cell-cell signaling	8	0.00676	BP
	GO:0005085	Guanyl-nucleotide exchange factor activity	5	0.02023	MF	GO:0006952	Defense response	5	0.00728	BP
	GO:0043565	Sequence-specific DNA binding	11	0.03272	MF	GO:0030168	Platelet activation	3	0.01864	BP
	GO:0008201	Heparin binding	4	0.03502	MF	GO:0051258	Protein polymerization	3	0.03966	BP
	GO:0005178	Integrin binding	3	0.04652	MF	GO:0005576	Extracellular region	44	0.00000	CC
	GO:0006915	Apoptosis	13	0.00173	BP	GO:0005615	Extracellular space	13	6.0E-5	CC
	GO:0006950	Response to stress	7	0.00173	BP	GO:0005577	Fibrinogen complex	3	6.0E-5	CC
	GO:0007050	Cell cycle arrest	6	0.00788	BP	GO:0031093	Platelet α granule lumen	4	8.1E-4	CC
	GO:0045944	Positive regulation of transcription from RNA polymerase II promoter	7	0.01021	BP
	GO:0045740	Positive regulation of DNA replication	3	0.01720	BP
	GO:0008360	Regulation of cell shape	4	0.02121	BP
	GO:0008285	Negative regulation of cell proliferation	8	0.02486	BP
	GO:0000122	Negative regulation of transcription from RNA polymerase II promoter	7	0.02486	BP
	GO:0009611	Response to wounding	3	0.02698	BP
	GO:0030183	B cell differentiation	3	0.02698	BP
	GO:0007229	Integrin-mediated signaling pathway	5	0.02698	BP
	GO:0006954	Inflammatory response	7	0.02698	BP
	GO:0007179	Transforming growth factor β receptor signaling pathway	4	0.02698	BP
	GO:0043066	Negative regulation of apoptosis	4	0.02698	BP
	GO:0006935	Chemotaxis	5	0.04499	BP
	GO:0007010	Cytoskeleton organization and biogenesis	5	0.04841	BP
	GO:0006955	Immune response	10	0.04843	BP
	GO:0005576	Extra cellular region	31	9.0E-5	CC
	GO:0005615	Extra cellular space	14	6.6E-4	CC
	GO:0005622	Intracellular	29	0.00843	CC
	GO:0005737	Cytoplasm	40	0.03660	CC

ONTO-TOOLS/OE2GO was used to identify the differentially expressed GO terms based on the hypergeometric distribution and corrected P value (< 0.05). The GO identified number (GOID), GO term name (GO name), the number of genes changed within each functional gene category, P values are listed. GO terms with at least 3 genes changed and corrected P values < 0.05 are listed in Table 4.