Table 1 Over and under-represented sites in pathways. Pathways in which over- and under-represented sites were identified for "target" transcription factors – TFs that receive the signal through the pathway in focus. Corresponding PWMs are shown.
From: Beyond microarrays: Finding key transcription factors controlling signal transduction pathways
Pathway in TRANSPATH® | TF (family) | TRANSFAC® PWM acc | p-value |
|---|---|---|---|
Overrepresented sites in pathways | |||
mTOR --> S6& eIF-4E | STAT | M00777 | 9.51E-003 |
MHC class II -> NF-AT | NF-AT | M00935 | 1.92E-004 |
IFNgamma -> STAT1alpha | STAT | M00777 | 6.27E-003 |
BCR -> c-Jun | AP-1 | M00517 | 8.91E-003 |
BCR -MLK3-> c-Jun | AP-1 | M00517 | 6.61E-003 |
TNF-alpha -> NFkappaB | NF-kappaB | M00774 | 9.86E-003 |
VEGF-A -> NF-ATc | NF-AT | M00935 | 7.31E-003 |
15d-PGJ2 -> PPAR-gamma | p300 | M00033 | 7.16E-003 |
G1 phase (Cdk4) | E2F | M00738 | 9.53E-004 |
S phase (Cdk2) | E2F | M00738 | 6.96E-006 |
IL-1beta -> c-Jun | AP-1 | M00517 | 2.89E-003 |
MKK6 -> p53 | p53 | M00761 | 8.64E-003 |
MKP-5 -/p53; MKK4 -> p53 | p53 | M00761 | 7.47E-003 |
Caspase-3 -/p53 | p53 | M00761 | 9.81E-003 |
p53 pathway | AhR | M00976 | 7.59E-003 |
HIF-1alpha pathway | AhR | M00976 | 2.34E-003 |
IL-1 pathway | AP-1 | M00517 | 6.57E-003 |
E2F network | E2F | M00738 | 7.73E-006 |
T-cell antigen receptor pathway | Ets/Elk-1 | M00971 | 7.44E-005 |
TLR4 pathway | p300 | M00033 | 4.29E-003 |
stress-associated pathways | Ebox; AP-1 | M01034; M00517 | 5.96E-03; 1.26E-03 |
EDAR pathway | NF-kappaB | M00774 | 8.90E-004 |
wnt pathway | Ets | M00971 | 7.10E-003 |
TNF-alpha pathway | NF-kappaB | M00774 | 9.03E-003 |
EDA-A2 -TRAF3-> NF-kappaB | NF-kappaB | M00774 | 2.31E-004 |
EDA-A1 -> NF-kappaB | NF-kappaB | M00774 | 2.31E-004 |
dsRNA -> IRF-7:IRF-3:CBP:p300 | p300; IRF | M00033; M00972 | 6.90E-03; 2.30E-03 |
TLR3 pathway | NF-kappaB | M00774 | 5.27E-004 |
dsRNA -> p50:RelA | NF-kappaB | M00774 | 1.35E-003 |
LPS -> IRF-3:IRF-7:CBP:p300 | p300 | M00033 | 4.86E-004 |
p38 pathway | STAT; Ebox; CREB/ATF | M00777; M01034; M00981 | 5.88E-04; 5.14E-03;2.33E-03 |
JNK pathway | AP-1 | M00517 | 9.24E-003 |
p38alpha -> MITF | Ebox | M01034 | 9.11E-003 |
Fas -/SRF | SRF | M01007 | 6.57E-004 |
PRL pathway | STAT; FOX | M00777; M00809 | 7.43E-03;6.85E-03 |
PRL -PI3K-> AKT | FOX | M00809 | 1.97E-005 |
Underrepresented sites in pathways | |||
Rac1 -> c-Jun & Elk-1 | AP-1;Ets | M00172; M00971 | 4.92E-03;3.55E-03 |
insulin -> AKT-1 pathway | CREB | M00917 | 6.83E-003 |
EGF pathway | AP-1 | M00926 | 3.03E-003 |
insulin pathway | CREB | M00917 | 3.45E-003 |
Rac1 pathway | AP-1; Ets | M00172; M00971 | 8.14E-03; 7.46E-03 |
stress-associated pathways | Ets | M00971 | 8.44E-003 |
p38 pathway | STAT | M00777 | 1.70E-005 |
E1 -PIRH2-/p53 | p53 | M00761 | 6.57E-003 |
hypoxia pathways | p300 | M00033 | 6.45E-003 |