Fig. 4

Identification of functional super-modules through protein overlap analysis (A) Network representation of the selected functional modules. Nodes represent the selected modules designated by the original name of the gene ontology term. Node size indicates the number of proteins incorporated in the module and gradient color the overall impact, i.e., minimum % of transcripts altered by each knockdown, ranging between 20% (selection cut-off) and 36%. The bar plots within the nodes indicate the impact of each knockdown on the module (ranging from 20 to 50%). The height of the bars follows a linear scale that is preserved between plots, allowing for a comparison of the relative impact of individual genes on different modules. Overall and specific impact values for each module/gene are presented in Supplementary Data File 7. Edge width indicates the number of commonly altered transcripts between two modules. Modules were manually grouped into 7 "super-modules" (circles) based on edge density (common altered transcripts) and functional similarity of module names