Table 1 Details of identified strongest path(s) by the application using the KEGG background network
From: StrongestPath: a Cytoscape application for protein–protein interaction analysis
Pathway | # found genes | # pathway genes | FDR-corrected p value | List of found pathway genes |
|---|---|---|---|---|
BDNF | 4 | 2 | \(3.54\times {10}^{-3}\) | RAC1, TRAF1 |
EGFR | 11 | 10 | \(7.99\times {10}^{-10}\) | CBL, CBLB, CBLC, ERBB2, HRAS, JAK1, KRAS, MAPK1, MAPK3, SRC |
Hedgehog | 10 | 5 | \(1.20\times {10}^{-8}\) | ARBB2, PRKACA, SMO, STK36, SUFU |
IL-1 | 4 | 3 | \(1.35\times {10}^{-5}\) | MYD88, TAB1, TRAF6 |
IL-2 | 5 | 3 | \(5.05\times {10}^{-5}\) | JAK1, JAK2, JAK3 |
IL-3 | 4 | 3 | \(2.88\times {10}^{-5}\) | JAK1, JAK2, TYK2 |
IL-6 | 5 | 4 | \(6.37\times {10}^{-7}\) | JAK1, JAK2, TYK2, SOCS3 |
IL-7 | 5 | 2 | \(3.06\times {10}^{-4}\) | JAK1, JAK3 |
TCR | 26 | 15 | \(5.28\times {10}^{-12}\) | CHUK, FYN, IKBKB, IKBKG, MAP3K14, MAP3K7, MAPK1, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK9, MAP3K1, MAPK8 |
TGFB | 31 | 15 | \(1.74\times {10}^{-11}\) | MAPK1, MAPK3, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, RHOA, RPCK1, ROCK2, SMAD1, AKT1, MAPK8, RAF1, WWTR1, YAP1 |
TNF-alpha | 10 | 10 | \(5.28\times {10}^{-12}\) | CASPB, IKBKB, MAP3K1, MAPK10, MAPK8, MAPK9, TAB1, TRADD, TRAF2, TRAF6 |
WNT | 48 | 25 | \(5.32\times {10}^{-22}\) | CREBBP, CSNK2A1, CSNK2A2, CSNK2B, DVL1, DVL2, DVL3, EP300, GSK3B, MAPK10, MAPK8, MAPK9, PLCB1, PLCB2, PLCB3, PLCB4, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, AKT1, MAPK1, MAPK3, SRC |