Copyright
©2010 Baishideng.
World J Gastroenterol. Mar 21, 2010; 16(11): 1385-1396
Published online Mar 21, 2010. doi: 10.3748/wjg.v16.i11.1385
Published online Mar 21, 2010. doi: 10.3748/wjg.v16.i11.1385
Table 1 Number of different genes expressed at different time points compared with those of control AGS cells
Time point (h) | Up-regulation (n) | Down-regulation (n) | Total |
0.5 | 109 | 209 | 318 |
1 | 140 | 242 | 382 |
2 | 151 | 203 | 354 |
4 | 126 | 291 | 417 |
6 | 198 | 156 | 354 |
Table 2 Description of selected clustered genes from short time-series expression miner (STEM) using dataset2 as input
Cluster ID | Symbol | |||||||||
Profile 123 | C4ORF18 | USP47 | CYP2J2 | LGR5 | FLRT3 | LOC643031 | TMEM117 | CACHD1 | C12ORF48 | MTMR4 |
RBL2 | ZDHHC23 | TTC13 | NUFIP1 | FLJ30596 | AASDHPPT | C2ORF15 | PGBD2 | LRRC8D | EVI1 | |
SKP2 | ZNF318 | VPS13A | AMACR | ST6GAL1 | AMD1 | ELOVL6 | PGM2 | SLC35A5 | CBR4 | |
EPB41L4B | C1ORF25 | C1GALT1 | ATG4C | MERTK | FANCL | LRIG3 | RHPN1 | PIP5K1B | SEMA3C | |
P4HA1 | LOC653094 | SCAMP1 | PPAP2B | MGC12965 | UST | LRRC1 | DEPDC1 | DDC | ZNF278 | |
ITPR2 | LOC653857 | DIXDC1 | KIAA1799 | C17ORF58 | TLR4 | LOC645102 | CDCA1 | MINA | DNAJB14 | |
MRPL35 | SLC25A20 | ARRDC4 | TRUB1 | ARNTL | ZNF642 | CASP8 | TIGD2 | SLC33A1 | OTUD6B | |
SPATA7 | FBXO30 | HSDL1 | GLE1L | LOC642432 | MGC33214 | PRKCQ | DPY19L3 | AKAP11 | LOC653783 | |
SGOL2 | PMS1 | GABPA | TCF12 | BMP4 | KNTC2 | BCKDHB | MANEA | GRHL3 | ATP2C1 | |
HIF1A | PEX1 | MTBP | ASF1A | SLC4A7 | PDIK1L | C4ORF13 | MAP3K1 | MOBK1B | MRRF | |
C7ORF25 | MPHOSPH9 | LOC159090 | PTK9 | B3GALT3 | COG6 | TMED7 | TMEM19 | LOC90693 | FLJ12078 | |
RP11-311P8.3 | ZNF181 | COG8 | KLHL23 | RFC3 | NBLA04196 | LOC653101 | TMTC4 | TDP1 | SCYL3 | |
PAQR3 | TMTC3 | BRD8 | NFE2L3 | PIGV | TSPAN12 | |||||
Profile 3 | PSG6 | FGB | CEACAM1 | CDKN1C | IFIT3 | RSAD2 | PSG7 | FLJ11286 | BTN3A2 | STAT1 |
FLJ20035 | ||||||||||
Profile 144 | EHD2 | RELB | COL16A1 | GDF15 | GNA15 | LETM2 | STX11 | FOSL1 | LOC647512 | SQSTM1 |
C12ORF59 | ADM2 | DDIT3 | CHAC1 | CSF2 | DDIT4 | |||||
Profile 12 | ZC3HAV1 | PSG9 | LYZ | FGG | PSG2 | PAGE4 | REG4 | GAD1 | PPM1H | TMEM70 |
LRP8 | PAQR8 | SH3BGRL | MYLIP | ROR1 | C5ORF14 | SUSD4 | MGC3265 | CADPS2 | IDUA | |
EPSTI1 |
Table 3 Statistically significant changed gene ontology of the four selected profiles
Profile | GO name | n | Corrected P value | Function code |
111 | Apical part of cell | 2 | 0.00842 | CC |
71 | Nucleic acid binding | 12 | 2.7E-4 | MF |
Zinc ion binding | 23 | 0.00308 | MF | |
Regulation of transcription | 22 | 0.01027 | BP | |
Myeloid cell differentiation | 2 | 0.01577 | BP | |
Nucleus | 39 | 2.9E-4 | CC | |
Intracellular | 23 | 3.5E-4 | CC | |
108 | Small GTPase binding | 2 | 0.01173 | MF |
Oxido-reductase activity | 6 | 0.02544 | MF | |
GPI anchor biosynthetic process | 2 | 0.02591 | BP | |
Female pregnancy | 3 | 0.02622 | BP | |
Golgi membrane | 5 | 0.03987 | CC | |
Cell surface | 3 | 0.03987 | CC | |
83 | DNA binding | 6 | 0.00577 | MF |
Metal binding | 6 | 0.03346 | MF | |
Nucleus | 10 | 0.01029 | CC |
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 |
Table 5 Top four significantly perturbed pathways at each time point
Time point | 0.5 h | 1 h | 2 h | 4 h | 6 h |
Gene mapping | |||||
Up-regulation | CAM | P53 | MAPK | CAM | CAM |
MAPK | TGF | ECHP | CY-CY | CY-CY | |
P53 | MAPK | RCC | MAPK | JAK-STA | |
TGF | CCC | P53 | JAK-STA | MAPK | |
Down-regulation | APP | APP | APP | Phos | APP |
Toll | CY-CY | CY-CY | APP | CY-CY | |
CY-CY | Toll | Toll | Toll | Toll | |
NKMC | Mela | Mela | Mela | Mela |
-
Citation: You YH, Song YY, Meng FL, He LH, Zhang MJ, Yan XM, Zhang JZ. Time-series gene expression profiles in AGS cells stimulated with
Helicobacter pylori . World J Gastroenterol 2010; 16(11): 1385-1396 - URL: https://www.wjgnet.com/1007-9327/full/v16/i11/1385.htm
- DOI: https://dx.doi.org/10.3748/wjg.v16.i11.1385