Figure 4

MA plots to show transcriptome-scale difference in genotype-dependent gene expression for loci with a normalized cut off of ≥ 10 tags in at least 1 test sample. A) Expression of all 23,460 loci in C600 versus Roberta genotype, of which 4,880 were differentially expressed as indicated. Expression values (normalised tag counts) were plotted on a log scale, so that the difference in expression is M = log₂R - log₂G and the average expression is A = 1/2 × (log₂R + log₂G); where R = C600 and G = Rob. B) Expression of all 13,125 large loci (> 500 bp with a tag count of > 10 in at least 1 sample) in C600 versus Roberta of which 1966 were differentially expressed as indicated.