Core stress responsive gene expression. The transcripts significantly (p < 0.05, PPDE > 0.96) increasing or decreasing in abundance in rice and Arabidopsis under drought, salt, cold and heat treated plants were overlapped based on their common response (Abiotic core - UP, DOWN, respectively). A) Genes which were part of these Abiotic core sets for rice and Arabidopsis were overlapped again in order to determine the number of transcripts with no orthologues (lightest gray shade), with known orthologues (darker gray shade) and the number of transcripts which were orthologous and showing a common (overlap) or opposite (overlap) response across all 4 abiotic stresses. ii) For each of the common and oppositely responding transcripts, the log2 fold change is shown for the control vs. treated as a heatmap, where red represents up-regulation and blue represents down-regulation. For Arabidopsis, only a single time point is shown, depending on which time point comparison was significant (Methods section). Genes indicated in bold were also analysed by qRT-PCR (as shown below). B) qRT-PCR results showing the log2 fold changes of 16 rice genes and 16 Arabidopsis genes in response to cold (dark red) and heat (green) stress. Note that these 16 genes represent orthologous genes in Arabidopsis and rice. The log2 fold changes based on the microarray data is also presented for comparison.