Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach
Figure 7
a. The reduced core network for the loss-loss analysis determined by pruning all edges with less than 5% support in the top 500 list of the Scale 2 analysis. Edge thickness and label represent the number of functional interactions between genes associated with the nodes being connected based on the STRING database. The tumor suppressor genes as defined by the Cancer Gene Census that map within the regions defined by the nodes are shown in rectangular insets. b. Representation of the 10 most enriched Ingenuity terms associated with the entire collection of genes that have a STRING interaction between the 17p region and 9p, 9q, 13q, 16q or 22q as determined by the Ingenuity software. The x-axis shows the −log transformed p value, corrected by the Benjamini Hochberg procedure as implemented in the Ingenuity software. c. Functional interaction enrichment is shown as a bar graph, which represent the ratio of interacting genes with respect to the total number of genes. P-values are determined using a Fishers' Exact test with randomly selected pairs of loci representing the null hypothesis. d. A functional interaction network around the nuclear co-repressor NCOR1 (also known as TRAC1) is shown. This network is a part of the network of interactors derived from the 17p interacting regions after removal of the canonical cancer genes TP53, RB1, CDKN2A and CDKN2B from the analysis. e. Illustration of the retroviral insertions mapped near CBFA2T3, recovered in a large screen of MuLV retroviral mutagenesis [11]. Insertions are shown as triangles. Blue triangles indicate insertions in the direction of transcription (plus), red triangles indicate insertions in the anti-transcription direction (minus). Insertions linked by dashed boxes are bi-allelic integrations recovered from the same tumor.