DGCA: A comprehensive R package for Differential Gene Correlation Analysis

BMC Systems Biology

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

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

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
WT Wildtype, Mut. Non-silent PTEN mutation

ISSN: 1752-0509