Figure 3

Categorical enrichment within the sub-networks comprising the S. mutans biofilms TRRN upon carolacton treatment. The co-regulated groups or sub-networks within the TRRN were found to be enriched with functional categories such as KEGG metabolic pathways, biological functional classes and gene ontology terms thus lending biological meaning to the inferred regulatory response network. Co-regulated groups denote sets of genes predicted to be commonly modulated by a transcription factor (indicated by filled pink rectangles). The regulatory response network also includes other transcriptional factors with only incoming connections (black rectangles in bold) and found to be among the co-regulated groups. Some of the co-regulated groups were found to be enriched with functional categories such as KEGG metabolic pathways (octagons), biological functional classes (circles) and gene ontology terms (triangles) whereas others (black circles filled in with letters ‘UK’) did not display any enrichment. Black edges with ellipsoid target edges represent relationships with dual regulation (some of the transcriptional regulatory relationships within the sub-network are characterized by positive (activational) expression patterns and others by inverted (repressive) expression patterns between the regulator and the target gene). The meanings of all the other arrow symbols are as described in the legend of Figure 2.