Table I. Quantified proteins significantly altered in gerbil gastric tissue following H. pylori infection that map to significantly altered biological pathways and networksa.
| Entry name | Gene | Accession number | Normalized fold change | log2 iTRAQ median | P value | BHb |
|---|---|---|---|---|---|---|
| Fatty acid-binding protein 1, liver | FABP1 | P12710 | 4.567 | 1.983 | 0.00E+00 | 0.000015 |
| Amine oxidase A | MAOA | Q64133 | 2.422 | 1.068 | 8.78E-07 | 0.000489 |
| Rho guanine nucleotide exchange factor 12 | ARHGEF12 | Q8R4H2 | 2.273 | 1.249 | 0.00E+00 | 0.000010 |
| Protein unc-13 homolog D | UNC13D | B2RUP2 | 2.135 | 0.886 | 2.08E-05 | 0.000756 |
| Spermine synthase | SMS | P97355 | 1.795 | 0.636 | 7.85E-04 | 0.001467 |
| Rab GTPase-binding effector protein 2 | RABEP2 | Q91WG2 | 1.485 | 0.635 | 8.44E-06 | 0.000301 |
| 60S ribosomal protein L31 | RPL31 | P62900 | 1.436 | 0.587 | 4.06E-05 | 0.000341 |
| Interleukin-1 receptor antagonist protein | IL1RN | P25085 | 1.411 | 0.561 | 9.01E-05 | 0.000391 |
| DNA-(apurinic or apyrimidinic site) lyase | APEX1 | P28352 | 1.402 | 0.552 | 1.18E-04 | 0.000451 |
| Zyxin | ZYX | Q62523 | 1.398 | 0.548 | 1.32E-04 | 0.000461 |
| Casein kinase II subunit beta | CSNK2B | P67871 | 1.386 | 0.536 | 1.88E-04 | 0.000472 |
| BRCA1-A complex subunit BRE | BABAM2 | Q8K3W0 | 1.385 | 0.534 | 1.99E-04 | 0.000482 |
| Paired amphipathic helix protein Sin3a | SIN3A | Q60520 | 1.372 | 0.521 | 2.86E-04 | 0.000522 |
| Myosin-14 | MYH14 | Q6URW6 | 1.362 | 0.510 | 3.88E-04 | 0.000562 |
| Peptidyl-prolyl cis-trans isomerase | FKBP3 | Q62446 | 1.354 | 0.502 | 4.82E-04 | 0.000582 |
| Serine/threonine-protein phosphatase 2A | PPP2R5A | Q6PD03 | 1.350 | 0.498 | 5.36E-04 | 0.000602 |
| Regulatory-associated protein of mTOR | RPTOR | Q8K4Q0 | 1.347 | 0.494 | 5.96E-04 | 0.000632 |
| Phospholipase A2 | PLA2G1B | Q9Z0Y2 | 0.680 | −0.491 | 1.48E-05 | 0.000321 |
| Acidic mammalian chitinase | CHIA | Q91XA9 | 0.636 | −0.589 | 4.45E-07 | 0.000211 |
| Signal recognition particle 14 kDa protein | SRP14 | P16254 | 0.624 | −0.615 | 1.61E-07 | 0.000201 |
| Fatty acid-binding protein 5, epidermal | FABP5 | Q05816 | 0.595 | −0.685 | 8.64E-09 | 0.000130 |
| Membrane-associated guanylate kinase | MAGI3 | Q9EQJ9 | 0.594 | −0.686 | 8.27E-09 | 0.000120 |
| Proteasome activator complex subunit 4 | PSME4 | Q5SSW2 | 0.582 | −0.988 | 1.75E-03 | 0.001749 |
| Pyruvate carboxylase | PKLR | Q05920 | 0.582 | −0.989 | 1.72E-03 | 0.001734 |
| cAMP-dependent protein kinase catalytic subunit beta | PRKACB | P68181 | 0.581 | −0.991 | 1.68E-03 | 0.001719 |
| Mitogen-activated protein kinase 12 | MAPK12 | O08911 | 0.580 | −0.993 | 1.64E-03 | 0.001689 |
| Mitogen-activated protein kinase 8 | MAPK8 | Q91Y86 | 0.580 | −0.993 | 1.64E-03 | 0.001704 |
| Myosin light chain kinase 2 | MYLK2 | Q8VCR8 | 0.580 | −0.993 | 1.64E-03 | 0.001675 |
| Protein kinase C delta type | PRKCD | P28867 | 0.579 | −0.996 | 1.58E-03 | 0.001645 |
| Inhibitor of nuclear factor kappa-B kinase subunit alpha | CHUK | Q60680 | 0.578 | −1.000 | 1.51E-03 | 0.001630 |
| PDZ and LIM domain protein 3 | PDLIM3 | O70209 | 0.574 | −1.009 | 1.35E-03 | 0.001571 |
| ADP-ribosylation factor 3 | ARF3 | P61205 | 0.573 | −1.011 | 1.32E-03 | 0.001556 |
| Mitogen-activated protein kinase 9 | MAPK9 | Q9WTU6 | 0.563 | −1.038 | 9.42E-04 | 0.001512 |
| Glycosylphosphatidylinositol anchor attachment 1 protein | GPAA1 | Q9WTK3 | 0.561 | −0.769 | 1.81E-10 | 0.000050 |
| Ephrin type-B receptor 3 | EPHB3 | P54754 | 0.554 | −1.061 | 7.01E-04 | 0.001452 |
| Cyclin-dependent kinase 17 | CDK17 | Q8K0D0 | 0.542 | −1.091 | 4.72E-04 | 0.001304 |
| Twinfilin-1 | TWF1 | Q91YR1 | 0.540 | −1.096 | 4.42E-04 | 0.001260 |
| Polyadenylate-binding protein 1 | PABPC1 | P29341 | 0.540 | −1.097 | 4.36E-04 | 0.001245 |
| Eukaryotic translation initiation factor 2 subunit 1 | EIF2S1 | Q6ZWX6 | 0.535 | −1.110 | 3.65E-04 | 0.001186 |
| Signal recognition particle receptor subunit beta | SRPRB | P47758 | 0.530 | −1.125 | 2.97E-04 | 0.001141 |
| 60S ribosomal protein L4 | RPL4 | Q9D8E6 | 0.526 | −1.136 | 2.55E-04 | 0.001111 |
| 40S ribosomal protein S6 | RPS6 | P62754 | 0.521 | −1.149 | 2.13E-04 | 0.001067 |
| Myosin regulatory light chain 12B | MYL12B | Q3THE2 | 0.520 | −1.152 | 2.04E-04 | 0.001052 |
| Methylmalonate-semialdehyde dehydrogenase | ALDH6A1 | Q9EQ20 | 0.515 | −1.165 | 1.69E-04 | 0.001008 |
| Fibrinogen gamma chain | FGG | Q8VCM7 | 0.499 | −1.210 | 8.76E-05 | 0.000948 |
| Polypeptide N-acetylgalactosaminyltransferase 3 | GALNT3 | P70419 | 0.497 | −1.217 | 7.89E-05 | 0.000934 |
| GA-binding protein alpha chain | GABPA | Q00422 | 0.489 | −1.239 | 5.65E-05 | 0.000889 |
| cAMP-dependent protein kinase type II-alpha regulatory subunit | PRKAR2A | P12367 | 0.487 | −1.247 | 5.00E-05 | 0.000874 |
| Myosin regulatory light polypeptide 9 | MYL9 | Q9CQ19 | 0.480 | −1.268 | 3.60E-05 | 0.000845 |
| Proteasome activator complex subunit 1 | PSME1 | P97371 | 0.477 | −1.277 | 3.12E-05 | 0.000771 |
| Cytochrome c | CYCS | P62897 | 0.465 | −1.314 | 1.72E-05 | 0.000726 |
| Alpha-soluble NSF attachment protein | NAPA | Q9DB05 | 0.460 | −1.328 | 1.37E-05 | 0.000711 |
| Wiskott-Aldrich syndrome protein family member 2 | WASF2 | Q8BH43 | 0.454 | −1.346 | 1.01E-05 | 0.000667 |
| Phosphoenolpyruvate carboxykinase 2 | PCK2 | Q8BH04 | 0.454 | −1.347 | 9.98E-06 | 0.000652 |
| 5′-AMP-activated protein kinase catalytic subunit alpha-2 | PRKAA2 | Q8BRK8 | 0.440 | −1.394 | 4.47E-06 | 0.000593 |
| Plasminogen | PLG | P20918 | 0.412 | −1.488 | 8.20E-07 | 0.000474 |
| Fermitin family homolog 2 | FERMT2 | Q8CIB5 | 0.411 | −1.491 | 7.75E-07 | 0.000445 |
| Peroxiredoxin-2 | PRDX2 | Q61171 | 0.390 | −1.568 | 1.76E-07 | 0.000370 |
| 60S ribosomal protein L24 | RPL24 | Q8BP67 | 0.387 | −1.577 | 1.47E-07 | 0.000356 |
| Long-chain-fatty-acid–CoA ligase 5 | ACSL5 | Q8JZR0 | 0.386 | −1.582 | 1.33E-07 | 0.000341 |
| ADP-ribosylation factor 4 | ARF4 | P61750 | 0.343 | −1.752 | 3.69E-09 | 0.000252 |
| Cyclin-dependent kinase 2 | CDK2 | P97377 | 0.337 | −1.779 | 2.01E-09 | 0.000222 |
| Cathepsin D | CTSD | P18242 | 0.294 | −1.976 | 1.78E-11 | 0.000163 |
| Fatty acid-binding protein 4, adipocite | FABP4 | P04117 | 0.272 | −2.089 | 9.31E-13 | 0.000119 |
a 64 of the 166 (Supplemental Table I) quantified proteins significantly altered in gastric tissue following H. pylori infection map to significantly altered biological pathways and networks. These 64 pathways include inflammatory, proliferation, differentiation, apoptosis, cell cycle, cell-cell junctions, MAPK, and PI3K signaling pathways in addition to network analysis.
b p values were corrected for multiple comparisons by the Benjamini-Hochberg (BH) method (BH FDR p < 0.05) (20). After applying the multiple comparisons by the BH method, we allowed all quantified proteins with significant p values less than the BH correction. This resulted in the quantification of 166 proteins significantly altered in abundance following H. pylori infection, 64 of which are shown here.