Fig. 6
From: BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data
Identification of enriched pathways among differentially expressed genes. a Bar graph showing the results of over-representation analysis using the Pathway Enrichment Plot tab. The maximum number of pathways/categories to show was set to 10 and the enrichment padj value cutoff was set to < 1 × 10− 30. The gene count (x-axis) indicates the number of genes enriched in each pathway and colors indicate level of significance (padj). The pathways are plotted on the y-axis in order of increasing significance. b While the Pathway Enrichment Plot tab shows a bar graph or dot plot for only a subset of enriched pathways, the Pathway Enrichment Map tab shows all of the enriched pathways in an interconnected network map. The size of each node indicates the gene count (number of genes enriched in each category) and the color represents the padj value (the cutoff was set to < 1 × 10− 30). c The GSEA Plot tab generates a plot of the running enrichment score for a specified pathway/category. The plot for the category “cell cycle” is illustrated here. Currently only Reactome pathways/categories are supported for each of these figures. The input data for a-c is the filtered or unfiltered data from the Gene Table tab (we set the LFC to < 0 and the padj cutoff to < 0.05)