Table 4. Top 15 Ingenuity Canonical Pathways predicted to be enriched (p < 0.05) based on the integrated “verified” dataset.
| # | Ingenuity Canonical Pathways | Molecules | Rank, Cell extract | Rank, ER/Golgi | Rank, CM | Rank, Glad4U | Rank, BCCluster |
|---|---|---|---|---|---|---|---|
| 1 | Interferon Signaling | IFIT1, STAT1, IFIT3, ISG15, MX1, IFI35, BAX | 5 | 3 | Not predicted | 303 | 272 |
| 2 | Superoxide Radicals Degradation | SOD2, SOD3, CAT, NQO1 | 34 | 92 (n.s.) | 8 | 313 | Not predicted |
| 3 | Caveolar-mediated Endocytosis Signaling | HLA-A, ITGAV, DNM2, ITGB1, ITGA6, B2M, HLA-B, FLOT2 | 28 | 5 | 20 | 282 | 233 |
| 4 | Hepatic Fibrosis / Hepatic Stellate Cell Activation | NFKB2, IGFBP4, COL12A1, STAT1, CSF1, BAX, IL6, ICAM1, VEGFC, COL18A1, CXCL8, MYH9 | 200 (n.s.) | 197 (n.s.) | 2 | 4 | 8 |
| 5 | Role of Tissue Factor in Cancer | ITGAV, ITGB1, CSF1, ITGA6, CXCL1, YES1, VEGFC, CXCL8, ARRB1 | 100 (n.s.) | 19 | 34 | 27 | 15 |
| 6 | Role of IL-17F in Allergic Inflammatory Airway Diseases | NFKB2, CXCL6, CXCL10, CXCL1, IL6, CXCL8 | 275 (n.s.) | Not predicted | 11 | 120 | 242 |
| 7 | Putrescine Degradation III | ALDH3A2, IL4I1, ALDH3A1, ALDH1A3 | 19 | 45 | 149 (n.s.) | 348 (n.s.) | 336 (n.s.) |
| 8 | Tryptophan Degradation X (Mammalian, via Tryptamine) | ALDH3A2, IL4I1, ALDH3A1, ALDH1A3 | 21 | 47 | 154 (n.s.) | 351 (n.s.) | 340 (n.s.) |
| 9 | Ethanol Degradation IV | ALDH3A2, CAT, ALDH3A1, ALDH1A3 | 6 | 52 | Not predicted | 357 (n.s.) | 420 (n.s.) |
| 10 | Complement System | CFB, C3, C1QBP, C1S, C1R | Not predicted | 195 (n.s.) | 3 | Not predicted | 339 (n.s.) |
| 11 | Dopamine Degradation | ALDH3A2, IL4I1, ALDH3A1, ALDH1A3 | 27 | 59 | 168 (n.s.) | 320 | 362 (n.s.) |
| 12 | IL-8 Signaling | ITGAV, PLD3, CXCL1, GNG12, BAX, LASP1, RAC2, ICAM1, VEGFC, CXCL8 | 75 | 17 | 62 | 8 | 4 |
| 13 | Virus Entry via Endocytic Pathways | HLA-A, DNM2, ITGB1, ITGA6, B2M, HLA-B, RAC2 | 72 | 4 | 24 | 213 | 99 |
| 14 | Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses | EIF2AK2, NFKB2, C3, OAS3, OAS2, DDX58, IL6, CXCL8 | 59 | 128 (n.s.) | 23 | 55 | 166 |
| 15 | Pentose Phosphate Pathway | TKT, G6PD, PGLS | 8 | 26 | 26 | 380 (n.s.) | 391 (n.s.) |
Pathways were ranked based on the significance level. Subsequently, the overlap between the top 15 pathways, as defined based on the integrated “verified” dataset, and pathways predicted based on the individual proteomics datasets (CE, ER/Golgi, CM) and literature mined dataset was established. The respective rank for the overlapping pathways is indicated. Significant pathways with the rank ≤ 15 are marked in bold, while significant pathways with rank > 15 are marked in italics. (n.s. not significant results).