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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

Fig. 2

Navigation. Structured access to enrichment analysis results is provided by an index page that links overview graphics, a gene report that includes measures of differential expression for each gene under investigation, and the full flat gene set rankings for each executed method (and, optionally, their combination). In addition, a top table for each method is linked containing detailed set-based (SBEA page) and network-based (NBEA page) views of significant gene sets. The SBEA page for a gene set is composed of (1) an interactive volcano plot (fold change vs. DE p-value) allowing immediate identification of significant genes by mouse-over, and (2) two heatmaps displaying the expression of all set genes and the subset of significant genes. The NBEA page illustrates interactions within a gene set by projecting it onto the underlying regulatory network, and for KEGG gene sets by additionally highlighting corresponding pathway maps. Results of method combination are linked in a combined page that displays the combined ranking alongside the individual rankings, and which can be interactively sorted and filtered according to user-selected criteria. See Additional files 2, 3 and 4 for several application examples and the vignette of the EnrichmentBrowser package for details of the various options

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