Between time point transcriptome dynamics reveal different patterns of gene regulation in compatible and incompatible potato tuber – Phytophthora infestans interactions. MA plots (hybridization intensity plotted against the fold change in expression) displaying between time point transcriptome dynamics in nontransformed ‘Russet Burbank’ (WT) and transgenic SP2211 (+RB) lines in response to P. infestans. X-axes indicate mean gene expression levels [0.5*(log2(FPKM1)+log2(FPKM2))] across the two selected time points for each comparison. Y-axes indicate fold change values [log2(FPKM1/FPKM2), where FPKM1 represents the later time point and FPKM2 represents the earlier time point] across the selected time points. A: changes in WT transcriptome dynamics from 0 to 24 hpi; B: changes in WT transcriptome dynamics from 24 hpi to 48 hpi; C: changes in +RB transcriptome dynamics from 0 hpi to 24 hpi; D: changes in +RB transcriptome dynamics from 24 hpi to 48 hpi. Within each panel, colored dots represent genes that are significantly (FDR<0.001) differentially regulated among comparisons. Black dots represent genes that are not significantly differentially regulated. Note that the WT line shows mostly up-regulation of genes during later stages of infection (panel B) while the +RB line displays approximately equal up- and down-regulation of genes (panel D).