Table 1. Ontology for biological processes represented in the top 300 enriched proteins identified in post-IACC samples.
| Biological Process | REFLIST | Protein Hits | Expected | Fold Enrichment | Raw P-value | FDR |
|---|---|---|---|---|---|---|
| MAPK cascade (GO:0000165) | 340 | 34 | 5.36 | 6.34 | 1.15E-16 | 2.81E-14 |
| intracellular signal transduction (GO:0035556) | 1071 | 53 | 16.9 | 3.14 | 4.26E-13 | 5.20E-11 |
| signal transduction (GO:0007165) | 2318 | 83 | 36.57 | 2.27 | 1.91E-12 | 1.55E-10 |
| cell surface receptor signaling pathway (GO:0007166) | 1206 | 55 | 19.03 | 2.89 | 3.22E-12 | 1.97E-10 |
| developmental process (GO:0032502) | 1501 | 62 | 23.68 | 2.62 | 6.31E-12 | 3.08E-10 |
| response to stimulus (GO:0050896) | 2677 | 87 | 42.24 | 2.06 | 5.37E-11 | 2.19E-09 |
| negative regulation of apoptotic process (GO:0043066) | 99 | 15 | 1.56 | 9.6 | 2.81E-10 | 9.79E-09 |
| regulation of catalytic activity (GO:0050790) | 359 | 26 | 5.66 | 4.59 | 4.05E-10 | 1.24E-08 |
| cell communication (GO:0007154) | 2686 | 85 | 42.38 | 2.01 | 5.07E-10 | 1.38E-08 |
| transmembrane receptor PTK signaling pathway (GO:0007169) | 151 | 17 | 2.38 | 7.14 | 1.17E-09 | 2.86E-08 |
| regulation of phosphate metabolic process (GO:0019220) | 537 | 30 | 8.47 | 3.54 | 5.81E-09 | 1.18E-07 |
| regulation of molecular function (GO:0065009) | 441 | 27 | 6.96 | 3.88 | 5.69E-09 | 1.26E-07 |
| immune system process (GO:0002376) | 669 | 33 | 10.56 | 3.13 | 1.76E-08 | 3.31E-07 |
| apoptotic process (GO:0006915) | 336 | 22 | 5.3 | 4.15 | 5.09E-08 | 8.87E-07 |
| immune response (GO:0006955) | 383 | 23 | 6.04 | 3.81 | 1.10E-07 | 1.79E-06 |
| cell death (GO:0008219) | 356 | 22 | 5.62 | 3.92 | 1.32E-07 | 1.89E-06 |
| death (GO:0016265) | 356 | 22 | 5.62 | 3.92 | 1.32E-07 | 2.01E-06 |
| cell differentiation (GO:0030154) | 548 | 25 | 8.65 | 2.89 | 3.86E-06 | 4.70E-05 |
| biological regulation (GO:0065007) | 2985 | 79 | 47.1 | 1.68 | 3.82E-06 | 4.90E-05 |
| locomotion (GO:0040011) | 310 | 18 | 4.89 | 3.68 | 4.24E-06 | 4.92E-05 |
| response to external stimulus (GO:0009605) | 351 | 19 | 5.54 | 3.43 | 5.99E-06 | 6.64E-05 |
| regulation of biological process (GO:0050789) | 2463 | 67 | 38.86 | 1.72 | 1.05E-05 | 1.07E-04 |
| cytokine-mediated signaling pathway (GO:0019221) | 60 | 8 | 0.95 | 8.45 | 1.02E-05 | 1.09E-04 |
| biological adhesion (GO:0022610) | 356 | 16 | 5.62 | 2.85 | 2.55E-04 | 2.31E-03 |
| cell adhesion (GO:0007155) | 356 | 16 | 5.62 | 2.85 | 2.55E-04 | 2.40E-03 |
| angiogenesis (GO:0001525) | 18 | 4 | 0.28 | 14.08 | 3.35E-04 | 2.82E-03 |
| cellular component movement (GO:0006928) | 480 | 19 | 7.57 | 2.51 | 3.27E-04 | 2.85E-03 |
| protein phosphorylation (GO:0006468) | 81 | 7 | 1.28 | 5.48 | 4.43E-04 | 3.60E-03 |
| cell-cell adhesion (GO:0016337) | 141 | 9 | 2.22 | 4.05 | 5.77E-04 | 4.40E-03 |
| protein folding (GO:0006457) | 94 | 7 | 1.48 | 4.72 | 1.01E-03 | 7.48E-03 |
| response to stress (GO:0006950) | 653 | 22 | 10.3 | 2.14 | 1.19E-03 | 8.32E-03 |
| proteolysis (GO:0006508) | 448 | 17 | 7.07 | 2.41 | 1.68E-03 | 1.11E-02 |
| cell-matrix adhesion (GO:0007160) | 51 | 5 | 0.8 | 6.21 | 1.75E-03 | 1.13E-02 |
| cellular calcium ion homeostasis (GO:0006874) | 115 | 7 | 1.81 | 3.86 | 2.99E-03 | 1.82E-02 |
| response to interferon-gamma (GO:0034341) | 58 | 5 | 0.92 | 5.46 | 2.95E-03 | 1.85E-02 |
| cellular process (GO:0009987) | 8247 | 157 | 130.12 | 1.21 | 3.19E-03 | 1.90E-02 |
| behavior (GO:0007610) | 61 | 5 | 0.96 | 5.2 | 3.61E-03 | 2.10E-02 |
| induction of apoptosis (GO:0006917) | 41 | 4 | 0.65 | 6.18 | 5.16E-03 | 2.86E-02 |
| ectoderm development (GO:0007398) | 212 | 9 | 3.34 | 2.69 | 7.90E-03 | 4.10E-02 |
To analyse our proteomic data, we used Gene PANTHER (Protein ANnotation THrough Evolutionary Relationships) classification system (http://www.pantherdb.org/) that combines gene function, ontology, pathways and statistical analysis tools to analyze large-scale, genome-wide data from proteomics experiments. The False Discovery Rate (FDR) adjusts the value at which a test is considered “significant” based on the rank of the predicted level of significance.