Table 2 Details of identified strongest path(s) and sub-optimal strongest path(s) by the application using the STRING background network in four separate runs
From: StrongestPath: a Cytoscape application for protein–protein interaction analysis
Pathway | Iteration 1 | Iteration 2 | Iteration 3 | Iteration 4 | ||
|---|---|---|---|---|---|---|
#pathway genes/#found genes | FDR-corrected p value | List of found pathway genes | #pathway genes/#found genes | #pathway genes/#found genes | #pathway genes/#found genes | |
BDNF | 3/4 | \(2.31\times {10}^{-6}\) | GRB2, NGF, SHC1 | 7/12 | 12/21 | 14/28 |
EGFR | 6/8 | \(1.85\times {10}^{-8}\) | AKT1, CBL, GRB2, HRAS, JAK2, PIK3CA | 9/22 | 12/49 | 19/85 |
Hedgehog | 5/5 | \(2.34\times {10}^{-13}\) | DHH, HHIP, SHH, SMO, SUFU | 7/17 | 7/28 | 7/46 |
IL-1 | 4/5 | \(3.36\times {10}^{-9}\) | IKBKB, MAP3K7, TAB2, TRAF6 | 7/10 | 7/19 | 9/38 |
IL-2 | 2/6 | \(3.61\times {10}^{-4}\) | IL2, JAK2 | 6/15 | 8/25 | 8/31 |
IL-3 | 0/6 | \(1\) | 2/11 | 2/22 | 3/43 | |
IL-6 | 4/8 | \(7.17\times {10}^{-8}\) | AKT1, IL6, JAK1, JAK2 | 5/13 | 5/27 | 5/45 |
IL-7 | 1/5 | \(8.12\times {10}^{-3}\) | JAK3 | 4/12 | 4/15 | 4/33 |
TCR | 3/4 | \(2.32\times {10}^{-5}\) | IKBKB, MAP3K7, TNF | 4/7 | 4/9 | 5/20 |
TGFB | 8/8 | \(2.01\times {10}^{-14}\) | TGFB3, ZFYVE9, AKT1, AXIN1, FKBP1A, GSK3B, MTOR, NEDD4L | 9/11 | 13/37 | 16/150 |
TNF-alpha | 3/3 | \(8.82\times {10}^{-6}\) | IKBKB, IKBKG, TNF | 7/7 | 11/20 | 12/40 |
WNT | 3/3 | \(2.31\times {10}^{-6}\) | APC, AXIN1, WNT1 | 7/9 | 10/18 | 14/37 |