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Table 2 Gene sets in the p53 dataset with P-value ≤ 0.001 by any of the three methods

From: Comparative evaluation of gene-set analysis methods

Gene Set

Before standardization

After standardization

VSN

 

Global

Ancova

SAM-GS

Global

Ancova

SAM-GS

Global

Ancova

SAM-GS

ATM Pathway*

<0.001

<0.001

<0.001

<0.001

0.002

<0.001

0.001

0.001

<0.001

BAD Pathway**

<0.001

0.007

<0.001

<0.001

<0.001

<0.001

0.004

0.004

<0.001

Calcineurin Pathway$

0.068

0.084

<0.001

0.007

0.002

<0.001

0.004

0.005

0.011

Cell cycle regulator†

0.021

0.017

<0.001

0.002

0.001

<0.001

0.002

<0.001

0.003

Hsp27Pathway**

0.047

0.044

<0.001

<0.001

0.001

<0.001

0.011

0.005

<0.001

Mitochondria pathway**

0.002

0.002

<0.001

0.007

0.007

<0.001

0.013

0.006

<0.001

p53 signaling pathway*

0.112

0.101

<0.001

0.003

0.003

0.001

0.006

0.005

0.006

p53 _UP*

0.003

0.004

<0.001

<0.001

<0.001

<0.001

0.019

0.018

<0.001

p53 hypoxiaPathway*

0.626

0.622

<0.001

<0.001

<0.001

<0.001

0.044

0.041

<0.001

p53 Pathway*

0.142

0.150

<0.001

<0.001

<0.001

<0.001

<0.001

0.001

<0.001

Raccycd Pathway†

0.177

0.181

<0.001

0.001

<0.001

<0.001

0.004

0.009

0.006

Radiation_sensitivity*

0.119

0.135

<0.001

<0.001

<0.001

<0.001

0.014

0.020

<0.001

SA_TRKA_RECEPTOR‡

0.254

0.252

<0.001

0.001

<0.001

<0.001

0.004

0.001

0.006

bcl2family & reg. network**

0.102

0.100

0.001

0.001

0.005

<0.001

0.010

0.014

0.001

Cell cycle arrest†

0.099

0.099

0.001

0.027

0.018

0.005

0.003

0.005

0.007

Ceramide Pathway**

0.002

0.006

0.001

0.004

0.004

<0.001

0.001

0.001

<0.001

CR_DEATH*

0.001

0.004

0.008

0.029

0.017

0.004

0.143

0.108

0.005

  1. * pathway member
  2. ** apoptosis
  3. $ p53-induced proline oxidase mediates apoptosis via a calcineurin-dependent pathway
  4. † cell cycle
  5. ‡ integrated negative feedback loop between Akt and p53