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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