Figure 5

Network graph of conserved transcription signatures in cancer. a) 3D graph layout with labelling of main features in the network’s topology. A graph of 9,882 nodes and 184,563 edges was created at Pearson threshold r≥0.6. Clustering of the graph using the MCL algorithm resulted in 639 clusters ranging in size from 1,008 nodes to 4 nodes. A number of large clusters were shown to be highly enriched in genes associated with expression in individual cell types and/or associated with specific cellular functions. See Additional files 3 and 4 for details b) Collapsed cluster diagram showing the conserved gene network as a simplified 2D-network where single nodes represent a gene cluster and are sized according to the number of transcripts within the cluster, edges represent connections between members of each cluster. Nodes representing the main clusters have been coloured according to functional groupings. Blue - clusters represent those associated with housekeeping functions; green - clusters of genes which are directly involved in cell cycle progression or whose expression is in way some linked to it; pink - genes associated with the immune component of the tumour and yellow - other stromal elements. Smaller clusters enriched with genes of known function are also shown.