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Table 4 Differential correlations of genes with PTEN between non PTEN-mutated and PTEN-mutated samples

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

Gene PTEN WT Cor. PTEN Mut. Cor. z-score Empirical p-Value q-Value Classes
FASLG -0.076 0.628 3.816 0.0003 0.015 -/+
IPCEF1 -0.012 0.627 3.511 0.0008 0.021 0/+
PIK3CD 0.015 0.52 2.63 0.01 0.169 NonSig
FBXW7 0.0001 0.433 2.177 0.031 0.381 NonSig
STUB1 -0.075 -0.473 -2.06 0.041 0.381 NonSig
WWP2 -0.107 -0.482 -1.965 0.051 0.381 NonSig
MAPK3 0.013 -0.379 -1.934 0.054 0.381 NonSig
AKT1 0.077 -0.28 -1.71 0.087 0.492 NonSig
BCAR1 -0.025 -0.369 -1.696 0.09 0.492 NonSig
NCOA3 -0.055 0.272 1.566 0.116 0.573 NonSig
PARK7 -0.001 -0.301 -1.453 0.144 0.587 NonSig
CBL 0.069 0.36 1.444 0.147 0.587 NonSig
MVP 0.215 -0.082 -1.414 0.155 0.587 NonSig
SOS1 0.022 0.299 1.343 0.176 0.62 NonSig
ANAPC5 -0.068 0.195 1.246 0.209 0.65 NonSig
PIK3R1 0.309 0.065 -1.193 0.229 0.65 NonSig
RBL2 0.109 0.338 1.139 0.251 0.65 NonSig
CDC27 0.002 0.239 1.131 0.254 0.65 NonSig
SLC9A3R1 -0.065 -0.267 -0.975 0.323 0.65 NonSig
  1. The output of running DGCA on the PTEN pathway gene set in the breast cancer RNA-seq samples, comparing correlations of these genes with PTEN in PTEN-wildtype samples to correlations in PTEN-mutated samples. 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. 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 PTEN mutation