Figure 5. Contrasting timepoint specific expression profiles of the genes which alter only the magnitude of their gene expression in response to the change of photoperiod conditions and clustering the relative changes in expression over time.

(A) contrasts the direction of the 819 genes which alter just the magnitude of their gene expression and are DE (>2-fold difference and >10 mean normalised reads) at one or more timepoint. The principal chart plots the size of the overlaps between timepoints and the supplementary chart presents the number of genes DE (either up or down) in LD relative to SD for each timepoint. Membership within each group for individual genes, including non DE genes, is given in Table S8. (B) The standardised and clustered abundances (such that the average expression value is zero and the standard deviation is one) of all 4,694 genes which were classed as just altering the magnitude of their gene expression in response to the photoperiod shift clustered into 18 clusters using c-means clustering. The number of genes in each cluster is listed alongside. (C) Mean standardised abundance for clusters examined in more detail are plotted with cluster 1 selected for containing MtFTa1 which is expressed in LD at all timepoints but not SD and clusters 9 and 10 were selected as genes in these clusters are consistently higher in SD (blue and dotted) than in LD (orange and line). Mean standardised abundances for all clusters are plotted in Fig. S6.