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Fig. 3 | Genome Biology

Fig. 3

From: Convergent network effects along the axis of gene expression during prostate cancer progression

Fig. 3

Target genes and putative effectors. a Density plots of the FCs in the four grade groups for three selected proteins (ACPP, POSTN, LGALS3BP) among the 20 highest scoring (score: mean of the absolute FCs across all tumor samples) proteins. Vertical lines correspond to the average FC in each of the four grade groups. These proteins were selected as target genes to identify potential regulators. b Distributions of the Spearman correlations of the mRNA target gene FCs with the CNAs of the “filtered neighborhood order one” and the “complement,” for the three target genes. The first set/group consists of the target itself and of those neighbors in STRING with confidence above 0.2, while the second consists of the remaining network genes in STRING. Both sets are filtered out for genes subject to CNAs in less than four tumor samples. P values (in each of the titles) show the significance of the one-sided t test. c Heatmap of the CNA matrix reduced to the significant regulators of the target gene ACPP output by the fitted elastic net model (i.e., those with a non-zero beta coefficient). The columns are ordered based on the grade group while there is a hierarchical clustering of the rows. The added colorbar depicts the mRNA FCs of the target gene ACPP

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