Table 3.
List of the genes in significant canonical pathways (P ≤ 0.05).
| Ingenuity canonical pathways | −log(p-value) | Ratio | Molecules |
|---|---|---|---|
| Axonal guidance signaling | 5.60 | 6.4 × 10−2 | PRKACB, ADAMTS7, RGS3, GLI2, BMP2, PIK3R5, MMP13, WNT16, WNT6, FZD1, GLI3, NTRK1, FIGF, WNT4, ARPC3, MYL10, PPP3CA, ACE, KALRN, CXCR4, WNT2B, GIT1, PDGFB, MYL1, SEMA3A, NTRK3, FZD3, EPHA2, WNT11, SEMA7A |
| Hepatic fibrosis/hepatic stellate cell activation | 5.27 | 1.03 × 10−1 | IL8, MYH6, IFNGR2, MMP13, IL6, IFNAR2, MYH7B, MYL1, PDGFB, COL1A2, IGFBP3, EDNRA, FIGF, MYH1, IL4 |
| Role of Osteoblasts, Osteoclasts, and Chondrocytes in Rheumatoid Arthritis | 5.01 | 7.98 × 10−2 | CAMK4, SFRP2, SMAD9, BMP2, WNT2B, PIK3R5, WNT16, MMP13, WNT6, IL6, FZD1, ITGB3, BMPR1B, FZD3, WNT4, MAP2K3, WNT11, PPP3CA, IL4 |
| Ovarian cancer signaling | 4.80 | 9.86 × 10−2 | PRKACB, RPS6KB1, GJA1, FGF9, WNT2B, PIK3R5, WNT16, WNT6, FZD1, FZD3, EDNRA, WNT4, FIGF, WNT11 |
| Basal cell carcinoma signaling | 4.71 | 1.37 × 10−1 | GLI2, GLI3, BMP2, WNT2B, FZD3, WNT16, WNT4, WNT6, FZD1, WNT11 |
| Human embryonic stem cell pluripotency | 4.65 | 8.97 × 10−2 | BMP2, WNT2B, PIK3R5, WNT16, WNT6, FZD1, PDGFB, INHBA, BMPR1B, NTRK3, NTRK1, FZD3, WNT4, WNT11 |
| Bladder cancer signaling | 4.62 | 1.21 × 10−1 | MMP27, IL8, MMP23B, FGF18, FGF9, MMP13, FIGF, MMP11, FGF7, FGF13, FGF19 |
| Actin cytoskeleton signaling | 4.59 | 7.56 × 10−2 | MYH6, FGD3, FGF9, ACTB, ACTN2, PIK3R5, MYH7B, GIT1, TTN, MYL1, PDGFB, FGF13, FGF18, ARPC3, MYL10, FGF7, FGF19, MYH1 |
| Regulation of the epithelial-mesenchymal transition pathway | 4.51 | 8.38 × 10−2 | TWIST2, FGF9, WNT2B, PIK3R5, WNT16, WNT6, FZD1, FGF13, PYGO1, FGF18, FZD3, WNT4, MAP2K3, FGF7, WNT11, FGF19 |
| Role of NANOG in mammalian embryonic stem cell pluripotency | 3.76 | 9.65 × 10−2 | BMPR1B, SMAD9, BMP2, WNT2B, FZD3, PIK3R5, WNT16, WNT4, WNT6, FZD1, WNT11 |
| Role of macrophages, fibroblasts, and endothelial cells in rheumatoid arthritis | 3.57 | 6.02 × 10−2 | IL8, CAMK4, SFRP2, IL15, WNT2B, PIK3R5, WNT16, MMP13, WNT6, IL6, FZD1, PDGFB, IL16, TLR7, FZD3, WNT4, FIGF, MAP2K3, WNT11, PPP3CA |
| Clathrin-mediated endocytosis signaling | 3.25 | 7.18 × 10−2 | APOA1, FGF9, ACTB, PIK3R5, PDGFB, FGF13, ITGB3, ALB, FGF18, ARPC3, FIGF, FGF7, PPP3CA, FGF19 |
| Colorectal cancer metastasis signaling | 3.02 | 6.2 × 10−2 | PRKACB, WNT2B, PIK3R5, WNT16, MMP13, WNT6, IL6, FZD1, MMP27, MMP23B, FZD3, TLR7, WNT4, FIGF, MMP11, WNT11 |
| Agranulocyte adhesion and diapedesis | 2.87 | 6.99 × 10−2 | MMP27, IL8, MYH6, MMP23B, CXCR4, ACTB, CXCL14, MMP13, CCL20, MMP11, MYH7B, MYL1, MYH1 |
| Cellular effects of sildenafil (Viagra) | 2.84 | 7.48 × 10−2 | PRKACB, MYH6, CACNG1, CAMK4, ACTB, PDE5A, PDE4B, MYL10, MYH7B, MYL1, MYH1 |
| Calcium signaling | 2.76 | 6.13 × 10−2 | PRKACB, CHRNG, MYH6, HDAC4, CAMK4, TNNT3, TNNC1, TNNT2, MYH7B, PPP3CA, CASQ2, MYL1, MYH1 |
| Retinoate biosynthesis I | 2.58 | 1.35 × 10−1 | AKR1B10, ALDH1A3, SDR16C5, BMP2, ADH1C |
| Crosstalk between dendritic cells and natural killer cells | 2.53 | 8.42 × 10−2 | ACTB, IL15, TLR7, TNFSF10, CD83, IL6, HLA-DRB5, IL4 |
| Role of tissue factor in cancer | 2.48 | 7.83 × 10−2 | IL8, RPS6KB1, PIK3R5, MMP13, HBEGF, F7, FGA, STAT5B, ITGB3 |
| Inhibition of matrix metalloproteases | 2.37 | 1.25 × 10−1 | MMP27, MMP23B, THBS2, MMP13, MMP11 |
| Role of Wnt/GSK-3β signaling in the pathogenesis of influenza | 2.30 | 8.64 × 10−2 | WNT2B, FZD3, WNT16, WNT4, WNT6, FZD1, WNT11 |
| Atherosclerosis signaling | 2.26 | 6.62 × 10−2 | COL1A2, IL8, ALB, CXCR4, APOA1, PLA2G10, MMP13, IL6, PDGFB |
| TGF-β signaling | 2.15 | 7.87 × 10−2 | BMPR1B, AMH, SMAD9, BMP2, MAP2K3, VDR, INHBA |
| Superpathway of methionine degradation | 2.13 | 9.38 × 10−2 | CBS, MAT1A, MGMT, MCEE, CTH, CDO1 |
| Glioblastoma multiforme signaling | 2.10 | 6.1 × 10−2 | RPS6KB1, WNT2B, FZD3, PIK3R5, WNT16, WNT4, WNT6, FZD1, PDGFB, WNT11 |
| Cysteine biosynthesis III (mammalia) | 2.09 | 1.33 × 10−1 | CBS, MAT1A, MGMT, CTH |
| Extrinsic prothrombin activation pathway | 2.00 | 1.5 × 10−1 | F7, TFPI, FGA |
| FGF signaling | 1.99 | 7.69 × 10−2 | FGF18, FGF9, PIK3R5, MAP2K3, FGF7, FGF13, FGF19 |
| Communication between innate and adaptive immune cells | 1.94 | 6.42 × 10−2 | IL8, IL15, TLR7, CD83, IL6, HLA-DRB5, IL4 |
| Oncostatin M signaling | 1.89 | 1.14 × 10−1 | MMP13, OSMR, PLAU, STAT5B |
| ILK signaling | 1.89 | 5.73 × 10−2 | MYH6, PPP2R3A, ACTN2, ACTB, BMP2, PIK3R5, FIGF, MYH7B, MYL1, MYH1, ITGB3 |
| Coagulation system | 1.85 | 1.05 × 10−1 | F7, PLAU, TFPI, FGA |
| IL-4 signaling | 1.78 | 7.59 × 10−2 | RPS6KB1, IL13RA1, INPP5F, PIK3R5, HLA-DRB5, IL4 |
| Role of IL-17A in arthritis | 1.76 | 7.94 × 10−2 | IL8, PIK3R5, CCL20, MMP13, MAP2K3 |
| Wnt/β-catenin signaling | 1.75 | 5.75 × 10−2 | GJA1, SFRP2, PPP2R3A, WNT2B, FZD3, WNT16, WNT4, WNT6, FZD1, WNT11 |
| Cysteine biosynthesis/homocysteine degradation | 1.74 | 2.5 × 10−1 | CBS, CTH |
| HIF1α signaling | 1.65 | 6.54 × 10−2 | MMP27, MMP23B, PIK3R5, MMP13, FIGF, EGLN3, MMP11 |
| TREM1 Signaling | 1.64 | 7.04 × 10−2 | IL8, TLR7, CD83, IL6, STAT5B |
| PPARα/RXRα activation | 1.63 | 5.24 × 10−2 | PRKACB, GHR, HSP90AB1, APOA1, FASN, MAP2K3, IL6, STAT5B, TGS1, ABCA1 |
| RAR activation | 1.63 | 5.29 × 10−2 | PRKACB, SMAD9, ALDH1A3, SDR16C5, BMP2, ADH1C, IGFBP3, SNW1, STAT5B, ZBTB16 |
| Role of JAK family kinases in IL-6-type cytokine signaling | 1.54 | 1.11 × 10−1 | OSMR, IL6, STAT5B |
| Factors promoting cardiogenesis in vertebrates | 1.52 | 6.38 × 10−2 | BMPR1B, SMAD9, BMP2, FZD3, FZD1, WNT11 |
| Nitric oxide signaling in the cardiovascular system | 1.50 | 6.06 × 10−2 | PRKACB, CAMK4, HSP90AB1, CAV1, PIK3R5, FIGF |
| Neuroprotective role of THOP1 in Alzheimer's disease | 1.46 | 7.41 × 10−2 | PRKACB, NTS, TAC1, ACE |
| IL-15 production | 1.45 | 9.68 × 10−2 | IL15, IL6, IRF1 |
| Hematopoiesis from multipotent stem cells | 1.40 | 1.67 × 10−1 | IL15, IL4 |
| Integrin signaling | 1.39 | 4.83 × 10−2 | ACTN2, ACTB, ITGA8, CAV1, PIK3R5, ARPC3, TSPAN6, GIT1, TTN, ITGB3 |
| T helper cell differentiation | 1.39 | 6.94 × 10−2 | IFNGR2, IL6, GATA3, HLA-DRB5, IL4 |
| PTEN signaling | 1.37 | 5.26 × 10−2 | RPS6KB1, BMPR1B, GHR, INPP5F, NTRK3, NTRK1, PIK3R5 |
| Granulocyte adhesion and diapedesis | 1.36 | 5.14 × 10−2 | MMP27, IL8, MMP23B, CXCR4, CXCL14, CCL20, MMP13, MMP11, ITGB3 |
| AMPK signaling | 1.34 | 4.79 × 10−2 | PRKACB, CAB39, RPS6KB1, PPP2R3A, FASN, PIK3R5, MAP2K3, PFKM |
| Epithelial adherens junction signaling | 1.34 | 5.44 × 10−2 | MYH6, ACTN2, ACTB, ARPC3, PARD3, MYH7B, MYL1, MYH1 |
| Sonic hedgehog signaling | 1.34 | 9.09 × 10−2 | PRKACB, GLI2, GLI3 |
| Role of IL-17A in psoriasis | 1.33 | 1.54 × 10−1 | IL8, CCL20 |
| Growth hormone signaling | 1.33 | 6.58 × 10−2 | RPS6KB1, GHR, IGFBP3, PIK3R5, STAT5B |
| BMP signaling pathway | 1.33 | 6.25 × 10−2 | PRKACB, BMPR1B, CAMK4, SMAD9, BMP2 |
Up-regulated genes were indicated in bold letters, the other genes were down-regulated.