Fig. 3

Visualization examples for an overrepresentation analysis. Visualisation of transcription factors whose target genes are overrepresented among significantly upregulated Escherichia coli genes (GSE55662 Gene Expression Omnibus experiment), using the Regulon database [24]. Transcription factors regulating less than 3 or more than 400 target genes were excluded. A Lollipop chart: visualises the distribution of eFDR values (x-axis) < 0.05 for enriched transcription factors (y-axis). B Network representation: nodes represent enriched transcription factors (coloured based on eFDR values), while edges connect nodes sharing at least one target gene among the significantly upregulated genes, and are weighted by the number of such shared genes. C Heatmap: illustrates which elements (target genes, x-axis) belong to enriched ontologies (transcription factors, y-axis). Cell colours correspond to eFDR values