KEGG pathways and GO biological processes enriched in PVTT13 and T13. Only KEGG pathways were displayed. The full Table S4 can be found in the online version of this article
| Up-regulated pathways in PVTT13 | ||||||
| Pathway ID | Description | % | type | Count | P Value | genes |
| hsa05033 | Nicotine addiction | 1 | up | 10 | 3.98E-06 | CACNA1B, GABRA1, GABRA4, GABRG2, GABRG3, GABRR1, GRIA1, GRIA4, GRIN2B, SLC17A6 |
| hsa04080 | Neuroactive ligand-receptor interaction | 2.8 | up | 28 | 1.58E-05 | ADRA2C, AVPR1B, BDKRB1, CHRNB3, CRHR2, GABRA1, GABRA4, GABRG2, GABRG3, GABRR1, GLP1R, GLRA1, MCHR1, GRIA1, …… |
| hsa04723 | Retrograde endocannabinoid signaling | 1.3 | up | 13 | 0.00031623 | ADCY2, CACNA1B, GABRA1, GABRA4, GABRG2, GABRG3, GABRR1, GRIA1, GRIA4, KCNJ9, RIMS1, PLCB1, SLC17A6 |
| hsa04930 | Type II diabetes mellitus | 0.81 | up | 8 | 0.00063096 | CACNA1B, CACNA1E, IKBKB, KCNJ11, PKLR, ABCC8, ADIPOQ, MAFA |
| hsa04727 | GABAergic synapse | 1.1 | up | 11 | 0.001 | ADCY2, CACNA1B, GABRA1, GABRA4, GABRG2, GABRG3, GABRR1, GAD2, HAP1, GABBR2, SLC12A5 |
| hsa_M00415 | Fatty acid biosynthesis, elongation, endoplasmic reticulum | 0.41 | up | 4 | 0.00158489 | HACD3, ELOVL2, ELOVL7, HACD2 |
| hsa05032 | Morphine addiction | 1.1 | up | 11 | 0.00158489 | ADCY2, CACNA1B, GABRA1, GABRA4, GABRG2, GABRG3, GABRR1, KCNJ9, OPRM1, PDE1C, GABBR2 |
| hsa04724 | Glutamatergic synapse | 1.2 | up | 12 | 0.00316228 | ADCY2, GRIA1, GRIA4, GRIN2B, GRM3, GRM4, SLC1A6, HOMER1, PLCB1, SLC17A6, PLA2G4E, PLA2G4D |
| hsa00564 | Glycerophospholipid metabolism | 1 | up | 10 | 0.00630957 | CDS1, PLA2G1B, DGKI, LPGAT1, LYPLA1, AGPAT4, GPAM, PLA2G2F, PLA2G4E, PLA2G4D |
| hsa04911 | Insulin secretion | 0.91 | up | 9 | 1.00E-02 | ADCY2, GCG, GLP1R, KCNJ11, KCNN1, ABCC8, RIMS2, PLCB1, KCNU1 |
| Dwon-regulated pathways in PVTT13 | ||||||
| Pathway ID | Description | % | type | Count | P Value | genes |
| hsa04380 | Osteoclast differentiation | 4 | down | 31 | 1.00E-18 | ACP5, BTK, CSF1R, CYBB, FCGR1A, FCGR3A, FCGR3B, IL1R1, ITGB3, JUNB, LCP2, NCF4, PIK3CD, SPI1, SYK, TGFB1, FOSL1, SOCS1, …… |
| hsa04151 | PI3K-Akt signaling pathway | 5.1 | down | 40 | 1.00E-11 | CCND3, COL4A3, COL6A1, COL6A2, COL6A3, COL9A2, CSF1R, CSF3, CSF3R, LPAR1, FGF2, FGF7, FGF9, NR4A1, TNC, IGF1R, IL2RG, IL6, …… |
| hsa05144 | Malaria | 1.9 | down | 15 | 1.00E-11 | CR1, CSF3, GYPC, HBA1, HBA2, HBB, IL6, IL18, ITGB2, TGFB1, TGFB3, THBS1, THBS2 |
| hsa04062 | Chemokine signaling pathway | 3.5 | down | 27 | 1.00E-10 | ADCY7, CXCR5, CCR1, CCR5, CCR6, DOCK2, PTK2B, FGR, CXCL2, HCK, CXCR1, CXCR2, JAK2, PIK3CD, PLCB2, PRKCB, RAC2, CCL11, VAV1, …… |
| hsa04512 | ECM-receptor interaction | 2.3 | down | 18 | 1.58E-10 | CD44, COL4A3, COL6A1, COL6A2, COL6A3, COL9A2, TNC, ITGA4, ITGB3, ITGB4, ITGB7, ITGB8, RELN, THBS1, THBS2, ITGA8, GP6, LAMA1 |
| hsa05152 | Tuberculosis | 3.3 | down | 26 | 2.51E-10 | CD14, PLK3, CR1, CTSS, FCER1G, FCGR1A, FCGR3A, FCGR3B, IL6, IL10RA, IL18, ITGB2, JAK2, LSP1, SYK, TGFB1, TGFB3, TLR1, TLR2, TLR4, …… |
| hsa04510 | Focal adhesion | 3.3 | down | 26 | 2.51E-09 | CCND3, COL4A3, COL6A1, COL6A2, COL6A3, COL9A2, FLNA, TNC, IGF1R, ITGA4, ITGB3, ITGB4, ITGB7, ITGB8, PIK3CD, PRKCB, RELN, …… |
| hsa04145 | Phagosome | 2.8 | down | 22 | 7.94E-09 | CD14, CTSS, CYBB, FCGR1A, FCGR3A, FCGR3B, ITGB2, ITGB3, MPO, MSR1, NCF4, THBS1, THBS2, TLR2, TLR4, TUBA4A, MRC2, CORO1A, …… |
| hsa05140 | Leishmaniasis | 1.9 | down | 15 | 1.26E-08 | CR1, FCGR1A, FCGR3A, FCGR3B, ITGA4, ITGB2, JAK2, NCF4, PRKCB, PTGS2, TGFB1, TGFB3, TLR2, TLR4, NCF1 |
| hsa04611 | Platelet activation | 2.3 | down | 18 | 1.26E-07 | ADCY7, BTK, FCER1G, ITGB3, ITPR3, LCP2, P2RX1, PIK3CD, PIK3CG, PLA2G4A, PLCB2, PTGS1, SYK, TBXAS1, AKT3, PIK3R5, GP6, FERMT3 |
| hsa04666 | Fc gamma R-mediated phagocytosis | 1.9 | down | 15 | 3.16E-07 | DOCK2, FCGR1A, FCGR3A, HCK, INPP5D, PIK3CD, PLA2G4A, PRKCB, RAC2, SYK, VAV1, WAS, AKT3, LAT, NCF1 |
| hsa04060 | Cytokine-cytokine receptor interaction | 3.5 | down | 27 | 3.98E-07 | CXCR5, BMPR1B, TNFSF8, CCR1, CCR5, CCR6, CSF1R, CSF2RB, CSF3, CSF3R, CXCL2, IL1R1, IL2RG, IL6, CXCR1, CXCR2, IL10RA, IL18, …… |
| hsa04640 | Hematopoietic cell lineage | 1.9 | down | 15 | 6.31E-07 | CD4, CD14, CD22, CD37, CD44, CR1, CSF1R, CSF3, CSF3R, FCGR1A, IL1R1, IL6, ITGA4, ITGB3, MME |
| hsa04621 | NOD-like receptor signaling pathway | 2.6 | down | 20 | 0.000001 | CYBB, CXCL2, IFI16, IL6, IL18, ITPR3, MEFV, PLCB2, TLR4, PSTPIP1, RIPK3, LRP1, TRPV2, NLRC4, CARD9, ANTXR1, CARD6, NLRP12, …… |
| hsa04664 | Fc epsilon RI signaling pathway | 1.5 | down | 12 | 2.00E-06 | BTK, FCER1G, INPP5D, LCP2, PIK3CD, PLA2G4A, MAP2K3, RAC2, SYK, VAV1, AKT3, LAT |
| hsa04662 | B cell receptor signaling pathway | 1.5 | down | 12 | 3.16E-06 | BTK, CD22, CD72, INPP5D, PIK3CD, PRKCB, RAC2, SYK, VAV1, AKT3, LILRB3, DAPP1 |
| hsa05200 | Pathways in cancer | 4.1 | down | 32 | 3.16E-06 | ADCY7, COL4A3, CSF1R, CSF3R, DAPK1, LPAR1, FGF2, FGF7, FGF9, FZD2, GSTP1, IGF1R, IL6, MMP2, PIK3CD, PLCB2, PRKCB, PTCH1, PTGS2, …… |
| hsa04670 | Leukocyte transendothelial migration | 1.9 | down | 15 | 5.01E-06 | CYBB, PTK2B, ITGA4, ITGB2, MMP2, NCF4, PIK3CD, PRKCB, RAC2, TXK, VAV1, CXCR4, CLDN2, MYL9, NCF1 |
| hsa04933 | AGE-RAGE signaling pathway in diabetic complications | 1.8 | down | 14 | 5.01E-06 | COL4A3, CYBB, IL6, JAK2, MMP2, PIM1, PIK3CD, PLCB2, PRKCB, STAT5A, TGFB1, TGFB3, THBD, AKT3 |
| hsa04015 | Rap1 signaling pathway | 2.7 | down | 21 | 7.94E-06 | ADCY7, CSF1R, LPAR1, FGF2, FGF7, FGF9, FPR1, FYB, IGF1R, ITGB2, ITGB3, LCP2, PIK3CD, PLCB2, PRKCB, MAP2K3, RAC2, THBS1, LPAR2, …… |
| hsa04072 | Phospholipase D signaling pathway | 2.2 | down | 17 | 7.94E-06 | ADCY7, DGKA, LPAR1, PTK2B, FCER1G, CXCR1, CXCR2, PIK3CD, PIK3CG, PLA2G4A, PLCB2, SYK, LPAR2, AKT3, AGPAT2, PIK3R5, CYTH4 |
| hsa04974 | Protein digestion and absorption | 1.7 | down | 13 | 7.94E-06 | COL4A3, COL5A1, COL6A1, COL6A2, COL6A3, COL9A2, COL10A1, KCNN4, MME, PRCP, SLC8A1, SLC7A7, SLC7A8 |
| hsa05146 | Amoebiasis | 1.7 | down | 13 | 1.58E-05 | CD14, COL4A3, IL1R1, IL6, ITGB2, PIK3CD, PLCB2, PRKCB, TGFB1, TGFB3, TLR2, TLR4, LAMA1 |
| hsa05410 | Hypertrophic cardiomyopathy (HCM) | 1.5 | down | 12 | 2.00E-05 | ACE, IL6, ITGA4, ITGB3, ITGB4, ITGB7, ITGB8, SLC8A1, TGFB1, TGFB3, ITGA8, PRKAG2 |
| hsa05418 | Fluid shear stress and atherosclerosis | 2 | down | 16 | 2.00E-05 | BMPR1B, CYBB, GSTM2, GSTP1, IL1R1, ITGB3, MMP2, PIK3CD, RAC2, THBD, TP53, AKT3, KLF2, TRPV4, NCF1, GSTT2B |
| hsa05202 | Transcriptional misregulation in cancer | 2.3 | down | 18 | 3.16E-05 | RUNX2, CD14, CD86, CSF1R, DEFA3, DUSP6, FCGR1A, FUT8, GRIA3, ID2, IGF1R, IL6, ITGB7, MPO, SPI1, TP53, NR4A3, PROM1 |
| hsa05205 | Proteoglycans in cancer | 2.4 | down | 19 | 5.01E-05 | CD44, FGF2, FLNA, FZD2, HCLS1, IGF1R, ITGB3, ITPR3, MMP2, PIK3CD, PRKCB, PTCH1, TGFB1, THBS1, TLR2, TLR4, TP53, AKT3, HPSE |
| hsa04630 | Jak-STAT signaling pathway | 2 | down | 16 | 6.31E-05 | CCND3, CSF2RB, CSF3, CSF3R, IL2RG, IL6, IL10RA, JAK2, LIF, PIM1, PIK3CD, STAT5A, STAT6, SOCS1, SOCS3, AKT3 |
| hsa04810 | Regulation of actin cytoskeleton | 2.4 | down | 19 | 7.94E-05 | CD14, FGF2, FGF7, FGF9, NCKAP1L, ITGA4, ITGB2, ITGB3, ITGB4, ITGB7, ITGB8, PIK3CD, RAC2, VAV1, WAS, ITGA8, MYL9, BAIAP2, FGD3 |
| hsa05134 | Legionellosis | 1.2 | down | 9 | 7.94E-05 | CD14, CR1, CXCL2, IL6, IL18, ITGB2, TLR2, TLR4, NLRC4 |
| hsa05150 | Staphylococcus aureus infection | 1.2 | down | 9 | 7.94E-05 | C1S, FCGR1A, FCGR3A, FCGR3B, FPR1, FPR2, CFH, ITGB2, PTAFR |
| hsa04514 | Cell adhesion molecules (CAMs) | 1.9 | down | 15 | 0.0001 | CD4, CD22, CD86, ICAM3, ITGA4, ITGB2, ITGB7, ITGB8, SIGLEC1, SPN, ITGA8, CLDN2, NLGN2, LRRC4, NTNG2 |
| hsa05145 | Toxoplasmosis | 1.7 | down | 13 | 0.0001 | CCR5, IL10RA, JAK2, PIK3CG, MAP2K3, TGFB1, TGFB3, TLR2, TLR4, SOCS1, AKT3, PIK3R5, LAMA1 |
| hsa05143 | African trypanosomiasis | 0.9 | down | 7 | 0.00012589 | HBA1, HBA2, HBB, IL6, IL18, PLCB2, PRKCB |
| hsa04010 | MAPK signaling pathway | 2.6 | down | 20 | 0.00031623 | CD14, DUSP6, FGF2, FGF7, FGF9, FLNA, NR4A1, IL1R1, GADD45B, PLA2G4A, PRKCB, MAP2K3, PTPN7, RAC2, TGFB1, TGFB3, TP53, …… |
| hsa04064 | NF-kappa B signaling pathway | 1.4 | down | 11 | 0.00031623 | BTK, CD14, CXCL2, IL1R1, GADD45B, PRKCB, PTGS2, SYK, TLR4, …… |
| hsa04750 | Inflammatory mediator regulation of TRP channels | 1.4 | down | 11 | 0.00039811 | ADCY7, HTR2B, IL1R1, ITPR3, PIK3CD, PLA2G4A, PLCB2, PRKCB, MAP2K3, TRPV2, TRPV4 |
| hsa04650 | Natural killer cell mediated cytotoxicity | 1.7 | down | 13 | 0.00050119 | PTK2B, FCER1G, FCGR3A, FCGR3B, ITGB2, LCP2, PIK3CD, PRKCB, RAC2, SYK, VAV1, NCR1, LAT |
| hsa04371 | Apelin signaling pathway | 1.7 | down | 13 | 0.00063096 | ADCY7, APLNR, CTGF, ITPR3, PIK3CG, PLCB2, SLC8A1, AKT3, KLF2, PIK3R5, PRKAG2, GNG2, GNB4 |
| hsa05323 | Rheumatoid arthritis | 1.3 | down | 10 | 0.00079433 | ACP5, CD86, IL6, IL18, ITGB2, TGFB1, TGFB3, TLR2, TLR4, TNFSF13B |
| hsa05414 | Dilated cardiomyopathy | 1.3 | down | 10 | 0.00079433 | ADCY7, ITGA4, ITGB3, ITGB4, ITGB7, ITGB8, SLC8A1, TGFB1, TGFB3, ITGA8 |
| hsa04672 | Intestinal immune network for IgA production | 0.9 | down | 7 | 0.001 | CD86, IL6, ITGA4, ITGB7, TGFB1, CXCR4, TNFSF13B |
| hsa05161 | Hepatitis B | 1.7 | down | 13 | 0.001 | EGR3, PTK2B, IL6, PIK3CD, PRKCB, STAT5A, STAT6, TGFB1, TGFB3, TLR2, TLR4, TP53, AKT3 |
| hsa04725 | Cholinergic synapse | 1.4 | down | 11 | 0.00125893 | ADCY7, ITPR3, JAK2, PIK3CD, PIK3CG, PLCB2, PRKCB, AKT3, PIK3R5, GNG2, GNB4 |
| hsa05321 | Inflammatory bowel disease (IBD) | 1 | down | 8 | 0.00125893 | IL2RG, IL6, IL18, STAT6, TGFB1, TGFB3, TLR2, TLR4 |
| hsa04014 | Ras signaling pathway | 2.2 | down | 17 | 0.00158489 | CSF1R, FGF2, FGF7, FGF9, IGF1R, PIK3CD, PLA2G4A, PRKCB, RAC2, AKT3, RASA3, LAT, GNG2, GNB4, RASAL3, RASGRP4, RASA4B |
| hsa04068 | FoxO signaling pathway | 1.5 | down | 12 | 0.00158489 | PLK3, IGF1R, IL6, GADD45B, PIK3CD, TGFB1, TGFB3, S1PR4, AKT3, KLF2, GADD45G, PRKAG2 |
| hsa05162 | Measles | 1.5 | down | 12 | 0.00158489 | CCND3, IL2RG, IL6, JAK2, PIK3CD, STAT5A, TLR2, TLR4, TP53, AKT3, RAB9B, TLR7 |
| hsa04066 | HIF-1 signaling pathway | 1.3 | down | 10 | 0.00199526 | CYBB, HK3, IGF1R, IL6, PFKFB3, PIK3CD, PRKCB, TIMP1, TLR4, AKT3 |
| hsa04350 | TGF-beta signaling pathway | 1.2 | down | 9 | 0.00199526 | BMP6, BMPR1B, ID2, INHBA, LTBP1, SMAD9, TGFB1, TGFB3, THBS1 |
| hsa04360 | Axon guidance | 1.8 | down | 14 | 0.00199526 | BMPR1B, DPYSL2, PIK3CD, PLXNB3, PTCH1, RAC2, RGS3, CXCR4, SEMA7A, SEMA4D, SEMA3C, LRRC4, SEMA4A, NTNG2 |
| hsa04080 | Neuroactive ligand-receptor interaction | 2.4 | down | 19 | 0.00251189 | ADORA3, APLNR, CHRNE, LPAR1, F2RL2, FPR1, FPR2, GPR35, GRIA3, HRH2, HTR2B, MC1R, NTSR1, OXTR, P2RX1, PTAFR, PTGDR, S1PR4, …… |
| hsa04620 | Toll-like receptor signaling pathway | 1.3 | down | 10 | 0.00251189 | CD14, CD86, IL6, PIK3CD, MAP2K3, TLR1, TLR2, TLR4, AKT3, TLR7 |
| hsa04020 | Calcium signaling pathway | 1.8 | down | 14 | 0.00316228 | ADCY7, ATP2A3, PTK2B, HRH2, HTR2B, ITPR3, NTSR1, OXTR, P2RX1, PLCB2, PRKCB, PTAFR, SLC8A1, ORAI2 |
| hsa04668 | TNF signaling pathway | 1.3 | down | 10 | 0.00316228 | CXCL2, IL6, JUNB, LIF, PIK3CD, MAP2K3, PTGS2, SOCS3, AKT3, RIPK3 |
| hsa04726 | Serotonergic synapse | 1.3 | down | 10 | 0.00398107 | HTR2B, ITPR3, KCND2, PLA2G4A, PLCB2, PRKCB, PTGS1, PTGS2, GNG2, GNB4 |
| hsa04610 | Complement and coagulation cascades | 1 | down | 8 | 0.00501187 | C1S, CR1, F2RL2, CFH, ITGB2, THBD, PROCR, VSIG4 |
| hsa04071 | Sphingolipid signaling pathway | 1.3 | down | 10 | 0.00630957 | ADORA3, FCER1G, PIK3CD, PLCB2, PRKCB, RAC2, TP53, S1PR4, AKT3, SGPP2 |
| hsa04144 | Endocytosis | 2.2 | down | 17 | 0.00630957 | CCR5, CSF1R, IGF1R, IL2RG, CXCR1, CXCR2, TGFB1, TGFB3, WAS, WIPF1, CXCR4, RAB31, SPG20, PSD4, CYTH4, VPS37B, RAB11FIP1 |
| hsa04550 | Signaling pathways regulating pluripotency of stem cells | 1.4 | down | 11 | 0.00630957 | BMPR1B, FGF2, FZD2, ID2, IGF1R, INHBA, JAK2, LIF, SMAD9, PIK3CD, AKT3 |
| hsa04723 | Retrograde endocannabinoid signaling | 1.2 | down | 9 | 0.00630957 | ADCY7, GRIA3, ITPR3, PLCB2, PRKCB, PTGS2, GNG2, GNB4, SLC17A8 |
| hsa04913 | Ovarian steroidogenesis | 0.77 | down | 6 | 0.00630957 | ADCY7, BMP6, CYP1B1, IGF1R, PLA2G4A, PTGS2 |
| hsa05142 | Chagas disease (American trypanosomiasis) | 1.2 | down | 9 | 0.00630957 | ACE, IL6, PIK3CD, PLCB2, TGFB1, TGFB3, TLR2, TLR4, AKT3 |
| hsa04115 | p53 signaling pathway | 0.9 | down | 7 | 0.00794328 | CCND3, CD82, GADD45B, PMAIP1, THBS1, TP53, GADD45G |
| hsa04540 | Gap junction | 1 | down | 8 | 0.00794328 | ADCY7, LPAR1, HTR2B, ITPR3, PLCB2, PRKCB, TUBA4A, TUBB6 |
| hsa05132 | Salmonella infection | 1 | down | 8 | 0.00794328 | CD14, FLNA, CXCL2, IL6, IL18, TLR4, WAS, NLRC4 |
| hsa05218 | Melanoma | 0.9 | down | 7 | 0.00794328 | FGF2, FGF7, FGF9, IGF1R, PIK3CD, TP53, AKT3 |
| hsa04659 | Th17 cell differentiation | 1.2 | down | 9 | 0.01 | CD4, IL1R1, IL2RG, IL6, JAK2, STAT5A, STAT6, TGFB1, LAT |
| hsa05130 | Pathogenic Escherichia coli infection | 0.77 | down | 6 | 0.01 | CD14, HCLS1, TLR4, TUBA4A, WAS, TUBB6 |
| hsa05412 | Arrhythmogenic right ventricular cardiomyopathy | 0.9 | down | 7 | 0.01 | ITGA4, ITGB3, ITGB4, ITGB7, ITGB8, SLC8A1, ITGA8 |