Figure 2

Examples of interactive tools. a) The Motif Browser tool (top dialog box) has here been used to search for TRANSFAC motifs containing the consensus sequence “CCAAT” (both orientations). The corresponding binding site predictions for the 15 motifs matching this criterion are shown as red boxes in the sequence browser partly visible in the background. The Positional Distribution Viewer tool (bottom dialog box) shows a histogram of the locations of these binding sites, and the prominent peak indicates that the majority of the sites are located within 200 bp upstream of the TSS. b) The Interactions Viewer tool. A part of a motif track is shown in close-up mode at 1200% scale (binding sites are displayed here without motif logos). The black binding site in the middle is the target site selected by the user and the red sites on either side have been highlighted by MotifLab as binding sites for transcription factors that are known to interact with the target factor(s) from other locations. All other binding sites are greyed out.