Figure 8

Analysis of putative motifs for core orthologous genes showing common response under abiotic stress. A) The occurrence of all possible 6-mers was calculated in each of the core orthologous up-regulated subsets for rice and Arabidopsis. The occurrence of each motif in a subset was made relative to the occurrence of that motif in all promoters in the respective genomes. Heat map intensity represents over (red) or under (blue) representation of putative motifs compared to the genome. From the 4,096 possible 6-mers, only the putative motifs present 20% more or less often than the percentage presence in the genome were visualised e.g. a value of 1.2 indicates that this motif in the respective subset occurs 20% more than the occurrence of this motif in the genome, whilst a value of 0.8 indicates that this motifs occurs 20% less than the percentage occurrence in the genome. Examples of conserved over-represented motifs within different stress subsets are indicated in the black boxes. B) The top 3 over-represented motifs from each of the up-regulated subsets are indicated on the heatmap by the coloured boxes. Note that motifs over-represented in the UP and DOWN regulated sets are indicated by an asterisk *. For the motifs representing known TF binding sites, the respective TF is annotated; the number in brackets indicates the associated reference. C) Examination of over/under-represented known 3'UTR motifs in each subset. Note that the number in brackets indicates the associated reference.