Table 3. The top 15 protein-sets from MSigDB C2 database for normal/tumor classification.
| Pathway | # Proteins | # Corr Genes | %Var | FDR |
| HSA05211 RENAL CELL CARCINOMA | 14 | 9 | 48 | 0.00041 |
| HSA04540 GAP JUNCTION | 10 | 6 | 44 | 0.0048 |
| HSA04662 BCR SIG PATH | 14 | 13 | 33 | 0.016 |
| HSA04070 PHOSPHATIDYLINOSITOL SIGNALING | 12 | 10 | 32 | 0.016 |
| INTEGRIN MEDIATED CELL ADHESION GENMAPP | 32 | 28 | 51 | 0.016 |
| HSA05220 CHRONIC MYELOID LEUKEMIA | 13 | 7 | 49 | 0.019 |
| HSA05120 EPITHELIAL CELL SIGNALING HP INF | 17 | 7 | 81 | 0.019 |
| METPATHWAY BIOCARTA | 24 | 20 | 55 | 0.019 |
| HSA05223 NON SMALL CELL LUNG CANCER | 12 | 6 | 52 | 0.019 |
| ST DIFFERENTIATION PATHWAY IN PC12 CELLS | 12 | 8 | 53 | 0.019 |
| HSA05215 PROSTATE CANCER | 13 | 6 | 52 | 0.019 |
| HSA05218 MELANOMA | 13 | 6 | 52 | 0.019 |
| HSA05213 ENDOMETRIAL CANCER | 13 | 6 | 52 | 0.019 |
| HSA05210 COLORECTAL CANCER | 14 | 8 | 50 | 0.019 |
| HSA04010 MAPK SIGNALING PATHWAY | 15 | 10 | 80 | 0.019 |
The protein-set name is listed in column 1. The number of proteins observed from that protein-set are reported in column 2. Column 3 reports the number of proteins within the protein-set that are most responsible for the differential phosphorylation of the metaprotein. Column 4 reports the percentage of the metaprotein's variation that is differential in tumor and normal tissue. Column 5 reports the FDR q-value measuring the significance of the differential phosphorylation of the metaprotein associated with the pathway in cancer.