Table 3.
Pathway enrichment results by using Metacore tool
| # | Networks | Total | p-value | FDR | In Data | Gene names |
|---|---|---|---|---|---|---|
| 1 | Cell cycle_G1-S Growth factor regulation | 195 | 3.776E-15 | 2.760E-13 | 21 | AKT3, GRB2, NF-kB, VEGF-A, EGFR, STAT3, c-Myc, Cyclin D, GSK3 alpha/beta, N-Ras, AKT(PKB), NF-kB p50/p50, AKT2, c-Raf-1, GSK3 beta, IRS-1, IGF-1 receptor, AKT1, Cyclin D1, NF-kB1 (p50), SMAD4 |
| 2 | Cell cycle_G1-S Interleukin regulation | 128 | 3.972E-15 | 2.760E-13 | 18 | AKT3, GRB2, NF-kB, STAT3, c-Myc, Cyclin D, GSK3 alpha/beta, N-Ras, AKT(PKB), NF-kB p50/p50, AKT2, c-Raf-1, GSK3 beta, Elk-1, IRS-1, AKT1, Cyclin D1, NF-kB1 (p50) |
| 3 | Development_Hemopoiesis, Erythropoietin pathway | 136 | 1.868E-13 | 8.656E-12 | 17 | GRB2, SHIP, NF-kB, STAT3, c-Kit, c-Myc, Cyclin D, N-Ras, AKT(PKB), Bim, NF-kB p50/p50, c-Raf-1, K-RAS, FOXO3A, Elk-1, AKT1, Cyclin D1 |
| 4 | Signal transduction_NOTCH signaling | 235 | 1.677E-11 | 5.215E-10 | 19 | GRB2, NF-kB, VEGF-A, NF-kB1 (p105), EGFR, STAT3, c-Myc, AKT(PKB), AKT2, c-Raf-1, Skp2/TrCP/FBXW, GSK3 beta, Cyclin D1, PTEN, mTOR, NF-kB1 (p50), SMAD4, FBXW7, HIF1A |
| 5 | Signal Transduction_TGF-beta, GDF and Activin signaling | 154 | 1.876E-11 | 5.215E-10 | 16 | SIP1 (ZFHX1B), GRB2, NF-kB, EGFR, RUNX2, c-Kit, c-Myc, AKT(PKB), c-Raf-1, IRS-1, IGF-1 receptor, Cyclin D1, mTOR, SMAD4, HIF1A, CREB1 |
| 6 | Signal transduction_ERBB-family signaling | 75 | 4.616E-11 | 1.069E-09 | 12 | GRB2, NF-kB, EGFR, STAT3, c-Myc, N-Ras, AKT(PKB), c-Raf-1, K-RAS, Elk-1, IRS-1, PTEN |
| 7 | Development_EMT_Regulation of epithelial-to-mesenchymal transition | 224 | 6.898E-11 | 1.254E-09 | 18 | SIP1 (ZFHX1B), GRB2, EGFR, TCF8, STAT3, EGR1, ROCK1, AKT(PKB), c-Raf-1, GSK3 beta, Elk-1, TNF-alpha, CTGF, PTEN, mTOR, SMAD4, HIF1A, CREB1 |
| 8 | Inflammation_IL-6 signaling | 119 | 7.216E-11 | 1.254E-09 | 14 | AKT3, GRB2, NF-kB, STAT3, c-Myc, AKT(PKB), NF-kB p50/p50, AKT2, c-Raf-1, 14-3-3 zeta/delta, Elk-1, AKT1, NF-kB1 (p50), 14-3-3 |
| 9 | Signal transduction_Leptin signaling | 107 | 2.434E-10 | 3.760E-09 | 13 | GRB2, NF-kB, VEGF-A, STAT3, EGR1, GSK3 alpha/beta, AKT(PKB), AKT2, c-Raf-1, IRS-1, AMPK alpha subunit, HIF1A, CREB1 |
| 10 | Cardiac development_Role of NADPH oxidase and ROS | 134 | 3.626E-10 | 4.742E-09 | 14 | GRB2, HDAC5, MEF2C, NF-kB, GSK3 alpha/beta, AKT(PKB), TBX3, c-Raf-1, GSK3 beta, SMAD5, Hamartin, PTEN, SMAD4, HIF1A |
| 11 | Reproduction_FSH-beta signaling pathway | 160 | 3.752E-10 | 4.742E-09 | 15 | NF-kB, VEGF-A, EGFR, EGR1, c-Myc, Cyclin D, AKT(PKB), c-Raf-1, IRS-1, IGF-1 receptor, CTGF, mTOR, SMAD4, HIF1A, CREB1 |
| 12 | Signal transduction_Androgen receptor signaling cross-talk | 72 | 5.284E-10 | 6.120E-09 | 11 | GRB2, NF-kB, EGFR, STAT3, AKT(PKB), c-Raf-1, FOXO3A, GSK3 beta, IGF-1 receptor, mTOR, CREB1 |
| 13 | Inflammation_Amphoterin signaling | 118 | 8.432E-10 | 9.015E-09 | 13 | ROCK, AKT3, NF-kB, NF-kB1 (p105), ROCK1, AKT(PKB), NF-kB p50/p50, AKT2, c-Raf-1, Elk-1, AKT1, TNF-alpha, NF-kB1 (p50) |
| 14 | Signal transduction_ESR1-membrane pathway | 91 | 6.908E-09 | 6.859E-08 | 11 | GRB2, EGFR, GSK3 alpha/beta, AKT(PKB), c-Raf-1, GSK3 beta, Elk-1, IRS-1, IGF-1 receptor, Cyclin D1, CREB1 |
| 15 | Inflammation_TREM1 signaling | 145 | 1.087E-08 | 1.007E-07 | 13 | AKT3, GRB2, MEF2C, NF-kB, EGR1, AKT(PKB), AKT2, c-Raf-1, 14-3-3 zeta/delta, Elk-1, AKT1, TNF-alpha, 14-3-3 |
| 16 | Translation_Regulation of initiation | 127 | 2.325E-08 | 1.968E-07 | 12 | AKT3, GRB2, EGFR, GSK3 alpha/beta, AKT(PKB), AKT2, c-Raf-1, GSK3 beta, IRS-1, Hamartin, AKT1, mTOR |
| 17 | Signal transduction_ESR1-nuclear pathway | 216 | 2.407E-08 | 1.968E-07 | 15 | GRB2, VEGF-A, NF-kB1 (p105), EGFR, c-Myc, AKT(PKB), AKT2, c-Raf-1, GSK3 beta, IRS-1, HDAC4, IGF-1 receptor, Cyclin D1, NF-kB1 (p50), SMAD4 |
| 18 | Development_Hedgehog signaling | 253 | 2.929E-08 | 2.262E-07 | 16 | GRB2, VEGF-A, TCF8, EGR1, c-Myc, Sirtuin1, ROCK1, c-Raf-1, Skp2/TrCP/FBXW, GSK3 beta, SMAD5, AKT1, Cyclin D1, SMAD4, FBXW7, CREB1 |
| 19 | Development_Regulation of angiogenesis | 222 | 3.480E-08 | 2.546E-07 | 15 | GRB2, NF-kB, VEGF-A, EGFR, TCF8, STAT3, c-Myc, AKT(PKB), c-Raf-1, CTGF, SMAD4, HIF1A, IGFBP7/8, CREB1, VEGFR-1 |
| 20 | Immune response_BCR pathway | 137 | 5.467E-08 | 3.800E-07 | 12 | GRB2, SHIP, NF-kB, EGR1, GSK3 alpha/beta, AKT(PKB), NF-kB p50/p50, c-Raf-1, Elk-1, PTEN, mTOR, NF-kB1 (p50) |
| 21 | Signal transduction_Nitric oxide signaling | 88 | 6.433E-08 | 4.258E-07 | 10 | NF-kB, VEGF-A, AKT(PKB), NF-kB p50/p50, c-Raf-1, Elk-1, IRS-1, CaMK II alpha, TNF-alpha, CREB1 |
| 22 | Inflammation_IL-13 signaling pathway | 91 | 8.902E-08 | 5.624E-07 | 10 | GRB2, STAT3, ARG1, c-Myc, AKT(PKB), c-Raf-1, Elk-1, IRS-1, NF-kB1 (p50), CREB1 |
| 23 | Immune response_TCR signaling | 174 | 9.726E-08 | 5.669E-07 | 13 | ROCK, GRB2, NF-kB, NF-kB1 (p105), ROCK1, AKT(PKB), Bim, NF-kB p50/p50, c-Raf-1, Elk-1, AKT1, TNF-alpha, NF-kB1 (p50) |
| 24 | Cell cycle_G2-M | 206 | 9.789E-08 | 5.669E-07 | 14 | AKT3, GRB2, EGFR, c-Myc, AKT(PKB), AKT2, DNMT1, c-Raf-1, Skp2/TrCP/FBXW, 14-3-3 zeta/delta, HDAC4, IGF-1 receptor, AKT1, 14-3-3 |
| 25 | Cardiac development_FGF_ErbB signaling | 124 | 1.804E-07 | 1.003E-06 | 11 | GRB2, MEF2C, EGFR, FOG2, Neurofibromin, AKT(PKB), TBX3, c-Raf-1, GSK3 beta, Versican, Hamartin |
| 26 | Inflammation_IL-10 anti-inflammatory response | 87 | 6.923E-07 | 3.701E-06 | 9 | NF-kB, STAT3, c-Myc, Cyclin D, AKT(PKB), NF-kB p50/p50, Cyclin D1, TNF-alpha, NF-kB1 (p50) |
| 27 | Inflammation_IL-4 signaling | 115 | 8.212E-07 | 4.228E-06 | 10 | GRB2, SHIP, NF-kB, AKT(PKB), Bim, c-Raf-1, GSK3 beta, Elk-1, IRS-1, PTEN |
| 28 | Signal Transduction_BMP and GDF signaling | 91 | 1.018E-06 | 5.054E-06 | 9 | RUNX2, c-Myc, AKT(PKB), YY1, AKT2, SMAD5, AKT1, SMAD4, CREB1 |
| 29 | Apoptosis_Anti-Apoptosis mediated by external signals via PI3K/AKT | 233 | 2.791E-06 | 1.338E-05 | 13 | GRB2, NF-kB, VEGF-A, EGFR, AKT(PKB), Bim, NF-kB p50/p50, FOXO3A, IRS-1, IGF-1 receptor, TNF-alpha, NF-kB1 (p50), VEGFR-1 |
| 30 | Inflammation_IL-2 signaling | 104 | 3.152E-06 | 1.461E-05 | 9 | GRB2, NF-kB, STAT3, AKT(PKB), NF-kB p50/p50, c-Raf-1, Elk-1, PTEN, NF-kB1 (p50) |
| 31 | Proliferation_Positive regulation cell proliferation | 221 | 9.263E-06 | 4.154E-05 | 12 | GRB2, VEGF-A, EGFR, STAT3, c-Kit, c-Myc, AKT(PKB), c-Raf-1, GSK3 beta, IGF-1 receptor, Cyclin D1, VEGFR-1 |
| 32 | Cardiac development_Wnt_beta-catenin, Notch, VEGF, IP3 and integrin signaling | 151 | 9.785E-06 | 4.250E-05 | 10 | MEF2C, VEGF-A, GSK3 alpha/beta, TBX3, c-Raf-1, GSK3 beta, Versican, MEF2, PTEN, VEGFR-1 |
| 33 | Development_Blood vessel morphogenesis | 228 | 1.272E-05 | 5.358E-05 | 12 | GRB2, NF-kB, VEGF-A, EGFR, STAT3, c-Myc, AKT(PKB), c-Raf-1, CTGF, HIF1A, IGFBP7/8, VEGFR-1 |
| 34 | Reproduction_Feeding and Neurohormone signaling | 210 | 3.159E-05 | 1.292E-04 | 11 | NF-kB, STAT3, c-Kit, c-Myc, AKT(PKB), c-Raf-1, Elk-1, TNF-alpha, mTOR, HIF1A, CREB1 |
| 35 | Proliferation_Negative regulation of cell proliferation | 184 | 5.446E-05 | 2.163E-04 | 10 | GRB2, KLF4, EGR1, Neurofibromin, c-Myc, Mxi1, c-Raf-1, Elk-1, IGF-1 receptor, Cyclin D1 |
| 36 | Immune response_IL-5 signalling | 38 | 7.474E-05 | 2.886E-04 | 5 | GRB2, STAT3, c-Myc, AKT(PKB), c-Raf-1 |
| 37 | Muscle contraction_Nitric oxide signaling in the cardiovascular system | 124 | 9.686E-05 | 3.639E-04 | 8 | MEF2C, VEGF-A, Sirtuin1, AKT(PKB), AMPK alpha 1 subunit, Elk-1, HIF1A, CREB1 |
| 38 | Apoptosis_Anti-Apoptosis mediated by external signals by Estrogen | 95 | 1.178E-04 | 4.309E-04 | 7 | GRB2, c-Myc, AKT(PKB), c-Raf-1, Elk-1, NF-kB1 (p50), CREB1 |
| 39 | Development_ERK5 in cell proliferation and neuronal survival | 24 | 1.597E-04 | 5.691E-04 | 4 | MEF2C, c-Myc, c-Raf-1, CREB1 |
| 40 | Proliferation_Lymphocyte proliferation | 210 | 1.643E-04 | 5.711E-04 | 10 | AKT3, GRB2, NF-kB, STAT3, AKT(PKB), AKT2, c-Raf-1, AKT1, TNF-alpha, mTOR |
| 41 | Cell adhesion_Integrin-mediated cell-matrix adhesion | 214 | 1.918E-04 | 6.280E-04 | 10 | ROCK, GRB2, Caveolin-2, c-Myc, ROCK1, AKT(PKB), c-Raf-1, GSK3 beta, Hamartin, Cyclin D1 |
| 42 | Reproduction_Progesterone signaling | 214 | 1.918E-04 | 6.280E-04 | 10 | GRB2, VEGF-A, EGFR, STAT3, c-Myc, c-Raf-1, GSK3 beta, IGF-1 receptor, AKT1, CREB1 |
| 43 | Inflammation_IgE signaling | 137 | 1.943E-04 | 6.280E-04 | 8 | GRB2, NF-kB, AKT(PKB), NF-kB p50/p50, c-Raf-1, Elk-1, TNF-alpha, NF-kB1 (p50) |
| 44 | Inflammation_Neutrophil activation | 215 | 1.992E-04 | 6.294E-04 | 10 | ROCK, GRB2, NF-kB, STAT3, ROCK1, AKT(PKB), NF-kB p50/p50, c-Raf-1, TNF-alpha, NF-kB1 (p50) |
| 45 | Inflammation_MIF signaling | 140 | 2.256E-04 | 6.967E-04 | 8 | GRB2, NF-kB, Cyclin D, NF-kB p50/p50, Cyclin D1, TNF-alpha, NF-kB1 (p50), CREB1 |
| 46 | Apoptosis_Anti-Apoptosis mediated by external signals via MAPK and JAK/STAT | 179 | 2.375E-04 | 7.176E-04 | 9 | GRB2, STAT3, EGR1, c-Myc, Bim, c-Raf-1, Elk-1, TNF-alpha, CREB1 |
| 47 | Inflammation_Protein C signaling | 108 | 2.628E-04 | 7.606E-04 | 7 | ROCK, NF-kB, ROCK1, AKT(PKB), NF-kB p50/p50, TNF-alpha, NF-kB1 (p50) |
| 48 | Signal transduction_ESR2 pathway | 77 | 2.727E-04 | 7.606E-04 | 6 | GRB2, VEGF-A, EGFR, c-Raf-1, AKT1, TNF-alpha |
| 49 | Apoptosis_Apoptosis stimulation by external signals | 144 | 2.736E-04 | 7.606E-04 | 8 | GRB2, SHIP, NF-kB, AKT(PKB), Bim, c-Raf-1, TNF-alpha, SMAD4 |
| 50 | Development_Skeletal muscle development | 144 | 2.736E-04 | 7.606E-04 | 8 | HDAC5, MEF2C, VEGF-A, Sirtuin, Histone deacetylase class II, Sirtuin1, HDAC4, MEF2 |
| Info | ||||||
| General | ||||||
| Date | 21/07/2018 | |||||
| Server | portal.genego.com | |||||
| Version | 6.35.69300 | |||||
| Workflow Settings | ||||||
| Type | Enrichment analysis | |||||
| Signals | both | |||||
| Active Data | ||||||
| Name | Type | Size | ||||
| 74_NetICS_mouse_data_hub_19_Jul_2018_genelist | General | 74 | ||||
Shown are pathway enrichment results generated by using Metacore version 6.35.69300 at 21.07.2018. The final list of predicted genes from NetICS were used (Table 2). Pathways are ranked based on the adjusted FDR P-value (column E) and the number and names of the pathway genes that are present in the final list of 74 predicted genes is given (column F-G).