Table 3.
Molecular pathway annotation, diabetic nephropathy.
| Pathway name | # Genes | Biomarker | Drug target | Enrichment |
|---|---|---|---|---|
| Angiogenesis | 148 | HSPB2, VEGFA, HSPB2-C11orf52 | JUN, VEGFA | No |
| Angiotensin II-stimulated signaling through G proteins and beta-arrestin | 35 | – | AGTR1 | No |
| Chemokine signaling | 190 | CCL2, NFKB1, CCL5 | CCL2 | Yes |
| Cholesterol biosynthesis | 11 | – | HMGCR | No |
| Complement and coagulation cascades | 69 | F2, FGB, MBL2 | SERPIND1, SERPINC1 | Yes |
| Cytokine-cytokine receptor interaction | 272 | CCL2, LEP, VEGFA, TNFRSF11B, CCL5, PRL, TGFB1 | CCL2, TGFB1, VEGFA, TNFSF12, IL18, IL1B, FLT1 | Yes |
| ECM-receptor interaction | 87 | SPP1, FN1 | – | Yes |
| Jak-STAT signaling | 158 | LEP, PRL | SOCS1 | No |
| MAPK signaling | 256 | TGFB1, FGF23, NFKB1 | CACNA1H, CACNA1I, CACNB4, CACNA1S, CASP3, CACNA2D3, TGFB1, CACNB3, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1F, CACNA1G, JUN, CACNB2, CACNG1, IL1B, CACNA2D1, CACNB1 | No |
| Metabolic pathways | 1165 | XYLT2, PTGDS, KL, PON1, PON2 | PTGS2, PDXK, QPRT, ALOX5, NT5E, IMPDH1, ACSL4, XDH, CES1, NNMT, ANPEP, HMGCR, IMPDH2, CYP11B2 | No |
| mTOR signaling | 61 | VEGFA | PDPK1, VEGFA, INS | No |
| NF-kappa B signaling | 90 | NFKB1 | PTGS2, IL1B | No |
| Oxidative stress response | 44 | – | JUN | No |
| PI3K-Akt signaling | 345 | SPP1, VEGFA, FN1, NFKB1, PRL, FGF23 | PDPK1, FLT1, VEGFA, INS | Yes |
| PPAR signaling | 71 | ADIPOQ | PPARG, ACSL4, FABP1, PDPK1, PPARA, ADIPOQ | No |
| Ras Pathway | 69 | – | PDPK1, JUN | No |
| Renin-angiotensin system | 17 | – | ACE2, AGTR1, REN, ANPEP, ACE | Yes |
| TGF-beta signaling | 80 | TGFB1, SMAD1 | TGFB1 | No |
| VEGF signaling | 62 | VEGFA | PTGS2, VEGFA | No |
| Wnt signaling | 139 | – | JUN | Yes |
| – | – | SPON2, WTAP, UMOD, LCN2, HP, VNN1, AGER, TGFBI, RBP4, NPHS1, HBA1, HBA2, DEFA1B, LPA, CST3, CTGF, ACTA1, PGC, S100A9, DPP4, ALB, CCKAR, GSTP1, DEFA3, S100A8, DEFA1, MMP9, CDH1, S100A4, NPPB, HAVCR1 | SOAT1, SLC6A4, ADORA1, MC2R, SIRT1, CYCS, RETN, EDNRA, CRH, EDNRB, KCNA1, ADORA2A, CALM2, CALM3, CALM1, PTX3, PDE3A, KCNMA1, P2RY12, SLC12A1, SLC12A3, GLP1R, DPP4, PDE5A, NR3C2, KCNJ11, ITGB2, KIF6, MMP9, CA12, TUBB1, NAMPT, HCAR3, HCAR2, AR, HBA1, HBA2, CA9, KCNH2, CA2, CA1, CASP1, TUBB, CA4, AHR, CTGF, ABCA1, PDE4A, PDE4B, SCN5A, MMP2, NPC1L1 | |
| Citrate cycle (TCA cycle) | 31 | – | – | No |
| General transcription regulation | 30 | – | – | No |
| Notch signaling | 48 | – | – | No |
| Oxidative phosphorylation | 122 | – | – | No |
| p38 MAPK | 34 | – | – | No |
| Pentose phosphate | 27 | – | – | No |
| Propanoate metabolism | 32 | – | – | No |
Provided is the KEGG pathway name, number of genes assigned to the pathway according to the pathway source, biomarker, and drug target candidates included in the pathway (gene symbols), and indication of significance of enrichment of such pathway on the basis of the consolidated DN kidney tissue transcriptomics data.