Supplementary Figure 8: Output from Example Recipe, “Find subnetworks of differentially expressed genes and identify associated biological functions.”
From: Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace
8a. Cytoscape network visualization of the top 50 genes differentially expressed between normal granulocyte/macrophage progenitor cells and leukemia stem cells. Nodes represent genes. Edges indicate pathways and interactions identified using the GeneMANIA functional association database. Subnetworks of highly connected nodes are identified using the MCODE algorithm and are displayed in the side panel. 8b. Cytoscape visualization of one such subnetwork. The bottom panel displays the names of genes found in the subnetwork along with metadata, e.g., descriptions and Gene Ontology (GO) Terms, associated with each gene. This subnetwork, for example, contains the SMAD1 gene, which is involved in the BMP signaling pathway.
