Figure 2

Binding profiles of the different NF-κB dimers. Heat map illustration of binding profiles obtained from microarray analysis of dimers. Within the heat map, probes that contain the 803 11-mer sequences and represent 'k-mer' space given by the consensus RGGRNNHHYYB can be found as rows whilst the nine NF-κB dimers have been organized into columns. A graded color scheme has been used to represent the ranked affinities of a dimer for a probe. From lightest to darkest this corresponds to decreasing affinity. Hierarchical clustering was used to describe relationships between binding profiles of the different dimers (Euclidean distance correlation; complete linkage analysis). The profile of RELARELA was largely distinct from those of the other eight dimers. On the whole, homodimers also have binding profiles that render these TFs to be less alike as a class. This is in contrast to the higher degree of similarity found between profiles within the heterodimer class. Two groups of sequences that contribute to similarities and differences between RELARELA and the other dimers have been used to construct representative binding models.