Table 2.
Significant pathways yielded from the analysis of full urine proteomics dataset (Approach-1) and after exclusion of plasma proteins (Approach-2). Pathways specific for Approach-1 are bolded and pathways specific for Approach-2 are underlined. The original lists of pathways obtained from both analyses can be found in the supplementary material.
| # | Pathway | #genes | coverage % | p-value | Genes up-regulated | Genes down-regulated |
|---|---|---|---|---|---|---|
| 1 | Platelet activation, signalling and aggregation | 23 | 10.45 | 2.55E-09 | A2M, ALB, APOA1, F2, PSAP, SERPINA1, SERPINF2, TF | CFL1, EGF, FN1, GNA11, GNAI1, GNAI2, GNB1, GNB2, IGF2, KNG1, MAPK3, PFN1, PIK3R3, RAP1A, SERPING1 |
| 2 | Platelet degranulation | 14 | 17.72 | 2.04E-08 | A2M, ALB, APOA1, PSAP, SERPINA1, SERPINF2, TF | CFL1, EGF, FN1, IGF2, KNG1, PFN1, SERPING1 |
| 3 | Response to elevated platelet cytosolic Ca2+ | 14 | 16.67 | 4.78E-08 | A2M, ALB, APOA1, PSAP, SERPINA1, SERPINF2, TF | CFL1, EGF, FN1, IGF2, KNG1, PFN1, SERPING1 |
| 4 | Scavenging of heme from plasma | 6 | 50.00 | 3.00E-06 | ALB, APOA1, HBA2, HBB, HP | AMBP |
| 5 | Vesicle-mediated transport | 19 | 7.95 | 1.31E-05 | ALB, APOA1, CLTCL1, HBA2, HBB, HP | AMBP, CHMP4B, CHMP5, MYH8, RAB10, RAB14, RAB5C, TSG101, VPS37B, VPS4B, VTA1, YWHAG, YWHAQ |
| 6 | Intrinsic Pathway of Fibrin Clot Formation | 6 | 27.27 | 2.05E-04 | A2M, F2, SERPINC1 | KNG1, SERPINA5, SERPING1 |
| 7 | Endosomal Sorting Complex Required For Transport (ESCRT) | 6 | 20.69 | 1.17E-03 | — | CHMP4B, CHMP5, TSG101, VPS37B, VPS4B, VTA1 |
| 8 | Formation of Fibrin Clot (Clotting Cascade) | 6 | 15.38 | 6.81E-03 | A2M, F2, SERPINC1 | KNG1, SERPINA5, SERPING1 |
| 9 | Binding and Uptake of Ligands by Scavenger Receptors | 6 | 15.00 | 7.88E-03 | ALB, APOA1, HBA2, HBB, HP | AMBP |
| 10 | Membrane Trafficking | 13 | 6.47 | 1.06E-02 | CLTCL1 | CHMP4B, CHMP5, MYH8, RAB10, RAB14, RAB5C, TSG101, VPS37B, VPS4B, VTA1, YWHAG, YWHAQ |
| 11 | Metabolism of Angiotensinogen to Angiotensins | 4 | 25.00 | 1.47E-02 | — | ACE, ANPEP, ENPEP, MME |
| 12 | ADP signalling through P2Y purinoceptor 12 | 4 | 18.18 | 2.25E-02 | — | GNAI1, GNAI2, GNB1, GNB2 |
| 13 | Signal amplification | 5 | 15.63 | 2.45E-02 | — | GNA11, GNAI1, GNAI2, GNB1, GNB2 |
| 14 | Thrombin signalling through proteinase activated receptors (PARs) | 5 | 15.63 | 2.45E-02 | F2 | GNA11, GNB1, GNB2, MAPK3 |
| 15 | Collagen formation | 7 | 8.14 | 2.75E-02 | COL11A1, COL11A2, COL15A1, COL17A1, COL22A1, COL4A4 | CTSB |
| 16 | Collagen biosynthesis and modifying enzymes | 6 | 9.38 | 3.31E-02 | COL11A1, COL11A2, COL15A1, COL17A1, COL22A1, COL4A4 | |
| 17 | Integrin cell surface interactions | 6 | 9.09 | 3.91E-02 | COL4A4 | AGRN, CD44, CDH1, FN1, HSPG2 |
| 18 | EPH-Ephrin signalling | 7 | 7.53 | 4.42E-02 | ACTB, CLTCL1 | ACTG1, ARHGEF7, CFL1, MYH9, SDCBP |
| 19 | Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | 4 | 19.05 | 4.49E-02 | F2 | IGF2, IGFALS, KLK1 |
| 20 | Complement cascade | 5 | 13.51 | 4.90E-02 | C3, C4A | C7, CD55, MASP2 |