Bernard et al. BMC Genomics 2010, 11:166 http://www.biomedcentral.com/1471-2164/11/166 Page 6 of 15 Figure 4 Sequence distance graph of the TC[-39,-26]-PLMs present in A. thaliana promoters. For each TC[-39,-26]-PLM observed in more than 200 A. thaliana promoters, the number of promoters containing the PLM is indicated above the sequence (surrounded data). In red PLMs observed in more than 350 promoters; in orange, PLMs in more than 200 promoters and in black PLMs observed in up to 200 sequences. TC[-39,- 26]-PLMs observed in more than 200 promoters are organized in an oriented and closed graph. Each edge between two PLMs reflects the presence of one substitution leading from one PLM to another. Edges between the less observed PLMs (in black) are not considered. The three seeds of this graph (in bold) are PLMs of which all the directly connected motifs are less frequently observed than the seed-PLMs themselves. Only one graph is possible. Figure 5 Presence in A. thaliana promoters of the three PLM classes characterized by a sharp functional window and preferentially located in the [-39, -26] region. The square represents the 14927 A. thaliana promoters (the whole promoter set) with experimentally known TSS. The central Venn diagram illustrates the overlaps between the three PLM classes in promoters. In the [-39, -26] region, 2606 promoters contained a canonical TATA-box, 4151 a TATAΔ-PLM and 2645 a TC[-39,-26]-PLM. In black the overlap between the three classes. In blue, the promoter sets analysed in the study, i.e. the promoter sets with PLMs from only one of the three classes and the promoter set that does not contain PLMs of the three classes.