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Table 2 Differential correlations of genes with TP53 between non p53-mutated and p53-mutated samples

From: DGCA: A comprehensive R package for Differential Gene Correlation Analysis

Gene

p53 WT Cor.

p53 Mut. Cor.

z-score

Empirical p-Value

q-Value

Classes

GNB2L1

0.257

0.01

-3.25

3.81E-05

0.008

+/0

RPS12

0.231

-0.002

-3.02

0.0001

0.009

+/0

TSC22D1

-0.027

0.227

2.97

0.0001

0.009

0/+

CDKN1A

0.019

0.227

2.73

0.0004

0.02

0/+

DGKA

0.057

0.252

2.58

0.0007

0.03

0/+

CARM1

0.172

-0.036

-2.24

0.0025

0.091

NonSig

DDB2

0.025

0.191

2.16

0.0033

0.094

NonSig

TNFRSF10B

0.194

0.034

-2.09

0.0043

0.094

NonSig

RPL18

0.158

-0.01

-2.05

0.0049

0.094

NonSig

ATF3

0.004

0.161

2.04

0.0051

0.094

NonSig

PYCARD

0.205

0.05

-2.04

0.0051

0.094

NonSig

TAX1BP3

0.305

0.156

-2.03

0.0052

0.094

NonSig

EI24

0.154

-0.007

-1.99

0.0059

0.097

NonSig

TNFRSF10C

0.179

0.03

-1.94

0.0069

0.097

NonSig

CCNG1

0.149

-0.092

-1.93

0.0072

0.097

NonSig

PML

0.016

0.163

1.92

0.0076

0.097

NonSig

CREBBP

0.153

0.006

-1.91

0.0077

0.097

NonSig

ABAT

0.145

-0.037

-1.88

0.0085

0.102

NonSig

NOL8

0.228

0.089

-1.85

0.0094

0.107

NonSig

  1. The output of running DGCA on the p53 pathway gene set in the breast cancer RNA-seq samples, comparing correlations of these genes with TP53 in p53-wildtype samples to correlations in p53-mutated samples, using the option to consider only positive correlations in calculating differential correlation between conditions. The top 20 gene pairs are shown here, while the rest are available in the Supplementary data. The “Classes” column indicates the correlation class of each of the gene pairs where, e.g., “+/0” indicates a significant (q < 0.05) positive correlation in the p53-wildtype samples and no significant correlation in the p53-mutated samples. Note that the significance for the correlations within each condition is not adjusted for multiple comparisons. 10,000 permutation samples were generated in order to estimate empirical p-values, using a pooled reference distribution approach, from which q-values were calculated
  2. WT Wildtype, Mut. Non-silent p53 mutation