Table 4 |
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|
The 31 gene sets for which SAM-GS and GSEA strongly disagreed (SAM-GS FDR ≤ 0.01, GSEA FDR ≥ 0.49) in the p53 analysis. |
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|
Gene Set |
GSEA |
SAM-GS |
p53 link |
||
|
|
|||||
|
FDR |
p-value |
FDR |
p-value |
||
|
|
|||||
|
ATM Pathway |
0.87 |
0.21 |
≤ 0.01 |
< 0.001 |
Pathway member |
|
BAD Pathway |
0.57 |
0.04 |
≤ 0.01 |
< 0.001 |
Apoptosis |
|
Calcineurin Pathway |
0.84 |
0.13 |
≤ 0.01 |
< 0.001 |
p53-induced proline oxidase mediates apoptosis via a calcineurin-dependent pathway (12) |
|
Cell cycle regulator |
0.90 |
0.29 |
≤ 0.01 |
< 0.001 |
Cell cycle |
|
Mitochondria pathway |
0.88 |
0.32 |
≤ 0.01 |
< 0.001 |
Apoptosis |
|
p53 signaling pathway |
0.51 |
0.01 |
≤ 0.01 |
< 0.001 |
Pathway member |
|
Raccycd Pathway |
0.83 |
0.56 |
≤ 0.01 |
< 0.001 |
Cell cycle |
|
SA_TRKA_RECEPTOR |
0.83 |
0.34 |
≤ 0.01 |
< 0.001 |
Integrated negative feedback loop between Akt and p53 (11) |
|
bcl2family and reg. network |
0.83 |
0.42 |
≤ 0.01 |
0.001 |
Apoptosis |
|
Cell cycle arrest |
0.98 |
0.49 |
≤ 0.01 |
0.001 |
Cell cycle |
|
Ceramide Pathway |
0.88 |
0.30 |
≤ 0.01 |
0.001 |
Apoptosis |
|
DNA DAMAGE SIGNALLING |
0.85 |
0.23 |
≤ 0.01 |
0.002 |
Pathway member |
|
SIG_IL4RECEPTOR IN_B_LYMPHOCYTES |
0.93 |
0.27 |
≤ 0.01 |
0.002 |
Cytokines; JAK/STAT signaling |
|
Cell cycle Pathway |
0.89 |
0.72 |
≤ 0.01 |
0.003 |
Pathway member |
|
G2 Pathway |
0.81 |
0.50 |
≤ 0.01 |
0.003 |
Pathway member |
|
Chemical Pathway |
0.53 |
0.04 |
≤ 0.01 |
0.005 |
Pathway member |
|
Drug resistance and metabolism |
0.86 |
0.08 |
≤ 0.01 |
0.005 |
Pathway member |
|
G1 Pathway |
0.81 |
0.37 |
≤ 0.01 |
0.005 |
Pathway member |
|
Breast cancer estrogen signaling |
1.00 |
0.85 |
≤ 0.01 |
0.006 |
Pathway member |
|
Ca_nf_at_signaling |
0.78 |
0.08 |
≤ 0.01 |
0.007 |
Apoptosis (and cytokines) |
|
Cytokine Pathway |
0.53 |
0.05 |
≤ 0.01 |
0.007 |
Cytokines |
|
ST_Interleukin_4_Pathway |
0.84 |
0.07 |
≤ 0.01 |
0.007 |
Cytokines; JAK/STAT signaling |
|
CR_DEATH |
0.86 |
0.31 |
≤ 0.01 |
0.008 |
Pathway member |
|
MAP00860: Porphyrin & chlorophyll metabolism |
0.92 |
0.29 |
≤ 0.01 |
0.010 |
CPO regulated by p53 (13) |
|
Ck1 Pathway |
0.49 |
0.02 |
≤ 0.01 |
0.011 |
Cdk5 phosphorylates p53 (9) |
|
Hivnef Pathway |
0.95 |
0.48 |
≤ 0.01 |
0.011 |
Apoptosis |
|
Ets Pathway |
0.79 |
0.45 |
≤ 0.01 |
0.012 |
Ets1 required for p53 transcriptional activation in UV-induced apoptosis (10) |
|
ST_Wnt_Ca2_cyclic_GMP_Pathway |
0.80 |
0.13 |
≤ 0.01 |
0.012 |
At least one known link between wnt and p53 (14) |
|
Chrebp Pathway |
0.84 |
0.42 |
≤ 0.01 |
0.013 |
unknown |
|
GPCRs_Class_A_Rhodopsin-like |
0.60 |
0.04 |
≤ 0.01 |
0.013 |
unknown |
|
ST_Fas_Signaling_Pathway |
0.80 |
0.52 |
≤ 0.01 |
0.013 |
Pathway member |
|
|
|||||
|
Dinu et al. BMC Bioinformatics 2007 8:242 doi:10.1186/1471-2105-8-242 |
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