Detection of TFBSs using two-way clustering. Starting from the available set of 34 TFBSs identified using sets of co-expressed genes (see text for details), clusters of genes with similar TFBS combinations in their promoter are delineated. Next, within each set of genes with similar TFBS content, groups of co-expressed genes are identified. Finally, motif detection is applied and evolutionarily conserved TFBSs are retained. The panel on the right shows the identification of the TFBS HA_HSE2 involved in zygotic embryogenesis. The top picture depicts a subset of all 573 Arabidopsis genes containing the module consisting of two distinct G-boxes. The two images below show the three groups of co-expressed genes and the newly identified TFBSs found in a set of 22 genes containing both G-boxes in their promoter and showing embryo-specific expression. Note that the section indicated with the dotted line corresponds with the motif-detection approach applied on co-expressed genes in the first stage.