Table 3.
Biological processes and KEGG pathway–enriched case biopsies with borderline changes in ECD compared to SCD, in ECD compared to LD, and in SCD compared to LD.
| Enriched biological processes and KEGG pathways | Transcripts increased in ECD vs. LD | Fold enrichment | Benjamini P |
|---|---|---|---|
| hsa04610: complement and coagulation cascades | F12, FGG, FGA, C3, CFB, FGB, F13A1, CFH | 7.37 | 0.00390 |
| hsa04512: ECM–receptor interaction | COL6A3, COL3A1, ITGB6, LAMC2, SV2B, ITGB3, COL1A1, THBS2, SPP1 | 6.81 | 0.00370 |
| hsa04060: cytokine–cytokine receptor interaction | LIF, INHBB, INHBA, TNFSF10, CCL13, IL6, IL2RA, OSMR, CXCL2, TNFRSF18, CCL18, IL11, CCL17 | 3.15 | 0.01960 |
| GO: platelet activation | FGG, IL6, SAA2, FGA, SAA1, FGB, COL3A1, IL11 | 18.28 | 0.00010 |
| GO: regulation of nuclear division, regulation of mitosis | NEK2, DLGAP5, BUB1, CENPF, IGF1, CENPE, CDC25C, CD28 | 10.45 | 0.00100 |
| GO: regulation of inflammatory response | FCER1A, F12, IL6, IL2RA, SAA2, SERPINF1, C3, OSMR, SAA1 | 8.66 | 0.00100 |
| GO: regulation of cell cycle process | NEK2, DLGAP5, CENPF, IGF1, CENPE, ANLN, BIRC5, UBE2C, CDC25C, GTSE1, LIF, BUB1, CD28 | 8.34 | 0.00000 |
| GO: coagulation, blood coagulation | F12, FGG, IL6, SAA2, FGA, SAA1, FGB, F13A1, COL3A1, ITGB3, IL11 | 7.89 | 0.00020 |
| GO: acute inflammatory response | F12, IL6, SAA2, C3, SAA1, CFB, CLU, CFH, SERPINA3, CD163 | 7.46 | 0.00090 |
| GO: hemostasis | F12, FGG, IL6, SAA2, FGA, SAA1, FGB, F13A1, COL3A1, ITGB3, IL11 | 7.45 | 0.00030 |
| GO: regulation of mitotic cell cycle | NEK2, DLGAP5, CENPF, IGF1, CENPE, ANLN, BIRC5, UBE2C, CDC25C, GTSE1, BUB1, MYC, CD28 | 6.25 | 0.00020 |
| GO: regulation of body fluid levels | F12, FGG, IL6, SAA2, FGA, SAA1, FGB, F13A1, COL3A1, ITGB3, AGR2, IL11 | 6.22 | 0.00050 |
| GO: wound healing | F12, IL6, F13A1, COL3A1, IGF1, ITGB3, CDH3, IL11, FGG, FGA, SAA2, FGB, SAA1, HMOX1, TM4SF4 | 5.74 | 0.00010 |
| GO: inflammatory response | NFKBIZ, F12, IL6, IL2RA, ELF3, CFB, C3, CLU, CXCL2, GAL, CCL18, CCL17, CD163, FOS, CCL13, SAA2, SAA1, STAB1, HMOX1, ITGB6, SERPINA3, CFH, PTX3, SPP1 | 5.40 | 0.00000 |
| GO: response to wounding | NRP1, ELF3, C3, F13A1, CLU, CXCL2, COL3A1, ITGB3, CDH3, IL11, FOS, FGG, SAA2, FGA, FGB, SAA1, HMOX1, ITGB6, CFH, SERPINA3, PTX3, SPP1, F12, NFKBIZ, IL6, IL2RA, CFB, IGF1, GAL, CCL18, CD163, CCL17, CCL13, LYVE1, STAB1, VCAN, TM4SF4 | 5.10 | 0.00000 |
| GO: defense response | ELF3, C3, CLU, CXCL2, HP, FOS, SAA2, SAA1, HMOX1, ITGB6, CFH, SERPINA3, LTF, PTX3, SPP1, F12, NFKBIZ, IL6, IL2RA, CFB, GAL, CCL18, HPR, CD163, CCL17, INHBB, INHBA, CCL13, CD19, LILRB5, STAB1, CTSG | 3.69 | 0.00000 |
| GO: cell adhesion, biological adhesion | OLFM4, NRP1, MYBPC2, NELL2, COL3A1, POSTN, ITGB3, SOX9, CDH3, CDH6, VCAM1, COL7A1, COL6A3, ITGB6, SPON2, LOXL2, THBS2, SPP1, COL15A1, CDHR4, LYVE1, STAB1, CD209, CPXM1, CLDN1, VCAN, LAMC2, ADAM12, HABP2 | 3.03 | 0.00010 |
| GO: immune response | C3, CLU, CXCL2, LIF, CFH, LTF, SPON2, PTX3, CD28, F12, TCF7, IL6, IL2RA, CFB, FOXJ1, RELB, IGJ, CCL18, CCL17, CCL13, TNFSF10, LILRB5, FCGR2B, CD209, CTSC, CTSG | 2.76 | 0.00090 |
| Transcripts increased in ECD vs. SCD | Fold enrichment | Benjamini P | |
| hsa04512: ECM–receptor interaction | TNC, COMP, COL6A3, SV2B, COL1A1, THBS2 | 8.30 | 0.04300 |
| GO: inflammatory response | CCL11, C1QB, FOS, CCL13, HIF1A, CEBPB, ADORA3, CCL8, C1S, GPR68, GAL, VSIG4, CHST1 | 4.40 | 0.01300 |
| GO: response to wounding | CEBPB, ADORA3, TNC, CCL8, GPR68, C1S, GAL, IL11, PLAUR, CHST1, CCL11, PCSK1, FOS, C1QB, CCL13, SLC1A3, HIF1A, SERPINE1, VSIG4 | 3.60 | 0.00100 |
| GO: defense response | ADORA3, CEBPB, KLRC3, CCL8, CD300C, COLEC12, GPR68, C1S, GAL, CHST1, CCL11, INHBA, FOS, C1QB, CCL13, HIF1A, LILRB5, TFF3, VSIG4 | 3.40 | 0.00500 |
| GO: cell adhesion | TNC, EMILIN2, SIGLEC14, COL16A1, CLDN14, ITGBL1, CCL11, NLGN4Y, COMP, CD33, SIGLEC7, COL6A3, MFAP4, ADAM12, THBS2, COL8A2, NTM, CDH11, SPON1 | 3.00 | 0.01300 |
| GO: biological adhesion | TNC, EMILIN2, SIGLEC14, COL16A1, CLDN14, ITGBL1, CCL11, NLGN4Y, COMP, CD33, SIGLEC7, COL6A3, MFAP4, ADAM12, THBS2, COL8A2, NTM, CDH11, SPON1 | 3.00 | 0.01100 |
| Transcripts increased in SCD vs. LD | Fold enrichment | Benjamini P | |
| hsa02010: ABC transporters | ABCA8, ABCB1, CFTR, ABCB4 | 17.12 | 0.03431 |
| hsa04610: complement and coagulation cascades | C8A, F12, FGG, CR2, F13A1 | 13.65 | 0.01873 |
| GO: regulation of lipid transport | APOA2, APOA1, APOC3, PON1 | 32.79 | 0.04672 |
| GO: mitosis, nuclear division | CCNB2, DLGAP5, CENPF, BIRC5, PBK, UBE2C, ASPM | 7.82 | 0.0386 |
| GO: response to wounding | C8A, F12, APOA2, FGG, CR2, F13A1, ITGB3, IGFBP1, CDH3, ADORA1, ORM2, SPP1 | 5.57 | 0.00526 |
Only the most significant GO terms associated with biological processes are shown.