Figure 3.
A meta-network of overlapping gene coexpression modules in human brain. Each node represents a module of coexpressed genes. Nodes are labeled with brain region and a module number. An edge between two nodes indicates a significant overlap of genes between two modules of different brain regions. Shown are only highly overlapping modules (p < 10−20). An overlap of three and more modules from different brain regions (e.g., ribosomes) indicates a cluster of highly conserved coexpression modules (represented by rectangular boxes with a dashed borderline). All overlapping modules within a cluster are overrepresented with genes from a major biological category shown in Table 1, such as neuron or TEs. In addition, several modules were clustered based on average GC content of their genes; GC-rich and GC-poor modules formed separate clusters. Several GC-poor modules were also overrepresented with “nucleus” genes. Thickness of connecting edges is proportional to the significance of the overlap. Module colors represent the direction and magnitude of regulation in alcoholic brain based on average t values (see Materials and Methods) (yellow, upregulation; blue, downregulation in alcoholics; intense colors, |t| > 1.8; light colors, |t| > 0.9).