Supplementary Figure 7: Representation of the workflow for the recipe "Find subnetworks of differentially expressed genes and identify associated biological functions.”

This cartoon workflow represents the recipe steps and includes three sections: (1) input data; (2) analyses completed in GenomeSpace tools (GenePattern and Cytoscape); and (3) the output of the recipe. Specifically, it passes an input gene expression dataset from two conditions or phenotypes (e.g., naïve and mature cells, tumor and normal) to GenePattern to find the list of the top 50 differentially expressed genes. Next, the GeneMANIA Cytoscape plugin is used to identify a network connecting these differentially expressed genes, derived from a resource collection of interaction networks, e.g., co-expression, co-localization, or protein-protein interactions. This network is then probed for highly interconnected subnetworks from which active underlying biological processes can be inferred, e.g., by consisting of genes with similar functional annotations.