Table 4

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.

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

Open Data