Table 4.
Pathway analysis of differentially expressed genes among cultured epithelial samples: CU2 and CU3 vs. CU1, CU3, and CU5
| Pathway (Identifiers Found) | Ratio | P Value* |
|---|---|---|
| Pathways with genes with increased expression in CU2 and CU3 | ||
| ECM organization (TIMP2, COL6A6, COL6A3, COL6A1, COLA1, COL4A1, COL4A2, ADAM12, DST, TEX10, COL18A1, SPARC. KALRN, COL16A1, LOXL1, LOXL2, HTRA1, LAMC1, PLOD3, LAMC2, PLOD2, PLOD1, P4HA2, SERPINE1, COL12A1, SDC2, PLCD3, FBN1, MFAP2, PMP2, FMNL1, BMP1, CRTAP, SERPINH1, LAMB1, COL5A2, MMP2, ITGA11, COL5A1, LAMB3, ITGA1) |
0.023 | 1.11E-16 |
| Collagen formation (SERPINH1, COL6A6, COL6A3, COL6A1, COL5A2, COL4A1, COL4A2, LAMB3, P3H2, P3H1, DST, PXDN, COL18A1, COL1A1, COL3A1, COL16A1, COL1A2, LOXL1, LOXL2, PLOD3, LAMC2, PLOD2, PLOD1, LAMA3, LOX, P4HA2, COL12A1, PLEC, COL27A1, FMNL1, BMP1, CRTAP) |
0.007 | 5.57E-14 |
| Non-integrin membrane-ECM interactions (LAMC1, SERPINH1, LAMB1, LAMC2, LAMA3, COL5A2, LAMA4, COL4A1, COL4A2, ITGB1, COL5A1, SDC2, LAMB3, DDR2, ITGA2, ITGB5, FN1, PDGFA, PDGFB, COL1A1, ACTN1, COL3A1, COL1A2, THBS1) |
0.004 | 1.06E-12 |
| Assembly of collagen fibrils and other multimeric structures (COL6A6, LAMC2, COL6A3, COL6A1, LAMA3, LOX, COL5A2, COL4A1, COL12A1, COL4A2, COL5A1, LAMB3, PLEC, DST, PXDN, COL18A1, COL1A1, COL27A1, COL3A1, BMP1, COL1A2, LOXL1, LOXL2) |
0.005 | 4.52E-11 |
| Collagen biosynthesis and modifying enzymes (SERPINH1, PLOD3, COL6A6, PLOD2, COL6A1, COL5A2, P4HA2, COL4A1, COL12A1, COL4A2, COL5A1, P3H2, P3H1, COL18A1, COL1A1, COL27A1, COL3A1, COL16A1, FMNL1, BMP1, COL1A2, CRTAP) |
0.005 | 1.04E-10 |
| Degradation of the ECM (TIMP2, LAMB1, COL6A6, COL6A3, COLA1, COL5A2, MMP2, COL4A1, COL4A2, COL5A1, LAMB3, A2M, FN1, MAN1A1, CTSK, TEX10, COL18A1, COL1A1, MMP12, MMP14, KALRN, COL3A1, COL16A1, COL1A2, MYH9, HTRA1, LAMC1, LAMC2, LAMA3, COL12A1, FBN1, ADAMTS1, CLSTN3, BMP1) |
0.01 | 1.64E-10 |
| ECM proteoglycans (LAMC1, LAMB1, COL6A6, COL6A3, COL6A1, LAMA3, COL5A2, LAMA4, COL4A1, SERPINE1, COL4A2, ITGB1, COL5A1, ITGA2, VCAN, ITGB5, ITGB6, SRGAP2, FN1, COL1A1, SPARC, COL3A1, COL1A2) |
0.005 | 5.48E-09 |
| Integrin-cell surface interactions (COL6A6, COL6A3, COL6A1, COL5A2, ITGA11, COL4A1, COL4A2, ITGA11, COL4A1, COL4A2, ITGB1, COL5A1, ITGA1, ITGA2, ITGB5, ITGA4, ITGA5, ITGB6, FBN1, FN1, COL18A1, COL1A1, COL3A1, COL16A1, COL1A2, THBS1) |
0.006 | 5.72E-09 |
| MET activates PTK2 signaling (LAMC1, LAMB1, LAMC2, LAMA3, COL5A2, LAMA4, ITGB1, COL5A1, LAMB3, ITGA2, FN1, COL1A1, COL27A1, COL3A1, COL1A2) |
0.002 | 6.03E-09 |
| Axon guidance (COL6A6, COL6A3, COL6A1, COL4A1, COL4A2, TNS1, TUBB6, CAP1, MYO5A, ABL2, GRB10, MYO5A, ABL2, GRB10, MYO9B, PSMD2, TPRA1, DLG1, KALRN, PPFIBP1, LAMC1, SLIT2, FAP, ABLIM3, SDC2, DPYSL2, SEMA5A, SPTBN1, FGFR1, LIMK1, MAPK11, EFNA1, LAMB1, FLNB, KIF3C, COL5A2, MMP2, COL5A1, ITGA1, ITGA2, ITGA5, SRGAP2, PDLIM7) |
0.04 | 7.77E-09 |
| Elastic fiber formation (LOX, COL4A1, ITGB1, EFEMP2, ITGB5, ITGA5, ITGB6, PLCD3, FBN1, FN1, LTBP2, MFAP2, BMP2, LTBP1, LOXL1, LOXL2) |
0.003 | 1.89E-08 |
| Regulation of IGF transport and uptake by IGFBPs (TIMP2, LAMB1, MMP2, COL4A1, LIMS1, FAM20C, FN1, APOE, CDH2, PAPPA, SPARC, LTBP1, LAMC1, CSF1, LOX, SDC2, VCAN, RCN1, LGALS1, GAS6, FBN1, MELTF, IGFBP6, CLSTN3, IGFBP4, EVA1A, CALU, FSTL3, FSTL1) |
0.009 | 4.59E-08 |
| MET promotes cell motility (LAMC1, LAMB1, LAMC2, LAMA3, COL5A2, LAMA4, ITGB1, COL5A1, LAMB3, ITGA2, TNS4, FN1, COL1A1, COL27A1, COL3A1, COL1A2) |
0.003 | 8.24E-08 |
| Collagen degradation (COL6A6, COL6A3, COL6A1, COL5A2, MMP2, COL4A1, COL12A1, COL4A2, COL5A1, CTSK, COL18A1, COL1A1, MMP12, MMP14, KALRN, COL3A1, COL16A1, COL1A2) |
0.005 | 2.62E-07 |
| Collagen chain trimerization (COL6A6, COL6A3, COLA1, COL5A2, COL4A1, COL12A1, COL4A2 COL5A1, COL18A1, COLA1, COL27A1, COL3A1, COL16A1, COL1A2) |
0.003 | 3.50E-07 |
| Posttranslational protein phosphorylation (TIMP2, LAMB2, COL4A1, LIMS1, FAM20C, FN1, APOE, CDH2, SPARC, LTBP1, LAMC1, CSF1, LOX, SDC2, VCAN, RCN1, LGALS1, GAS6, FBN1, MELTF, IGFBP4, EVA1A, CALU, FSTL3, FSTL1) |
0.008 | 4.20E-07 |
| Syndecan interactions (FN1, COL5A2, ITGB1, COL5A1, SDC2, COL1A1, ACTN1, ITGA2, COL3A1, COL1A2, ITGB5, THBS1) |
0.002 | 7.15E-07 |
| Signaling by receptor tyrosine kinases (SPRY2, COL6A6, COL6A3, COL6A1, COL4A1, COL4A2, TNS4, ADAM12, GRB10, APOE, SPARC, KALRN, LAMC1, ITPR2, LAMC2, PTPRK, ITPR3, AXL, SPTBN1, FGFR1, MAPK11, NEDD4, RALA, VEGFA, CAV1, LAMB1, FLNB, COL5A2, SPHK1, COL5A1, LAMB3, ITGA2, PAG1, RAB11FIP5, FN1, ANOS1, COL1A1, COL3A1, COL1A2, DNM1) |
0.038 | 7.62E-07 |
| Signaling by PDGF (COL6A6, COL6A3, COL6A1, COL5A2, COL4A1, COL4A2, COL5A1, RASA1, NT5DC2, PDGFC, PLAT, PDGFA, PDGFB, COL3A1, THBS3, THBS1) |
0.005 | 1.39E-06 |
| Laminin interactions (LAMC1, LAMB1, LAMC2, LAMA3, LAMA4, COL4A1, COL4A2, ITGB1, LAMB3, COL18A1, ITGA1, ITGA2) |
0.002 | 1.42E-6 |
| Pathways with genes with increased expression in CU1, CU3, and CU5 | ||
| Neutrophil degranulation (ANK3, PRKCD, NAPRT, CYBB, VAMP8, CD55, GSTK1, LRRC6, TUBB4B, S100P, LRG1, CD14, SELL, IDH, SERPINB3, SVIP, RIPOR2, CST3, HPSE, MGST1, CD9, ATP10B, SLCO4C1, FASN, FCGR2A, CSTB, LCN2, DEGS2, TACC2, NFASC, SERPINA1, CRACR2A, IQGAP2, STOM, METTL7A, CTSC, ALDH3B2, PLAC8, CEACAM6, CTSD) |
0.033 | 9.92E-4 |
| Termination of O-glycan biosynthesis (MUC13, MUC15, MUC16, RPIA, MUC1, MUC2, ST6GAL1, ST6GALNAC4, MUC5B, MUC5AC) |
0.002 | 1.37E-3 |
| Defective GALNT12 causes CRCS1 (MUC13, MUC15, MUC16, GLANT12, MUC1, MUC2, MUC5, MUC5AC) |
0.001 | 2.02E-3 |
| Metal sequestration by antimicrobial compounds (S100A7, S100A8, S100A9, TF. LCN2, LTF) |
0.001 | 3.62E-3 |
|
O-linked glycosylation of mucins (MUC13, MUC15, MUC16, RPIA, MUC1, MUC2, CHST4, ST6GALNAC4, GALNT6, GCNT3, B3GNT6, B3GNT3, GALNT12, GALNT14, ST6GAL1, MUC5B, MUC5AC) |
0.005 | 3.96E-3 |
| ERBB2 activates PTK6 signaling (NRG4, ERBB4, ERBB3, BTC) |
0.001 | 4.39E-3 |
| Fatty acids (CYP4B1, CYP2A13, RRAGD, CYP4F3, CYP2J2, CYP2F1, CYP4F12, SORL1, CYP4F11) |
0.002 | 5.74E-3 |
| ERBB2 regulates cell motility (NRG4, ERBB4, ERBB3, BTC) |
0.001 | 5.84E-3 |
| Defective GALNT3 causes familial hyperphosphatemic tumoral calcinosis (MUC13, MUC15M MUC16, MUC1, MUC2, MUC5B, MUC5AC) |
0.001 | 7.62E-3 |
| SHC1 events in ERBB2 signaling (MITF, NRG4, ERBB4, BTC) |
0.001 | 9.77E-3 |
| Defective GALNT3 causes familial C1GALT1C1 causes TNPS (MUC13, MUC15, MUC16, MUC1, MUC2, MUC5B, MUC5AC) |
0.001 | 9.77E-3 |
| GRB2 events in ERBB2 signaling (MITF, NRG4, ERBB4, BTC) |
0.001 | 9.77E-3 |
Ratio refers to percentage of the total genes in the pathway. CRCS1, colorectal cancer 1; CU, cultured epithelia; ECM, extracellular matrix; GALNT12, polypeptide N-acetylgalactosaminyltransferase 12; IGF, insulin-like growth factor; IGFBPs, IGF-binding proteins; MET, mesenchymal-epithelial transition factor; NBR, nasal brushing; PDGF, platelet-derived growth factor; PTK2, protein tyrosine kinase 2; TNPS, Tn polyagglutination syndrome.
*
P ≤ 0.01 after Benjamini-Hochberg multiple test correction.