Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach
Figure 5
Networks of co-occurring gain and loss.
The networks that result from hierarchical clustering of Scale 2 results are shown in different panels. Each panel represents either the gain-gain, loss-loss or gain-loss analysis. The resultant network is visualized using the Cytoscape software package (www.cytoscape.org). Edge thickness scales according to the number of co-occurrence links found between the two genomic loci. The size of the nodes is proportional to the highest rank found among the different individual loci that constitute a node. If only one genomic location is present in a node, i.e. this location did not cluster with any other locations, it is colored gray. The cancer gene enrichment among all genes mapping to the locations described by the nodes is shown in the top right hand corner. P-values are determined by Fisher's Exact test. The functional interaction enrichment of all genes between nodes that are linked with an edge is represented in the lower right hand corner of each panel. P-values are determined using Fishers' Exact test, with randomly generated pairs of loci representing the null hypothesis.