Comparison between 454 and Illumina mRNA-seq results. (A) Scatter plot of log2 transformed 454 and Illumina counts in WT and GPC-RNAi plants. Red lines represent the locally weighted polynomial regression (LOWESS method). (B) Volcano plots showing the magnitude of gene expression ratios (log2) as a function of the significance of the difference in expression between the two genotypes, is displayed on the y-axis [-log10(P-value at DESeq)]. Vertical red lines delimit two-fold up- and down-regulation and the horizontal blue line corresponds to a P-value cutoff of 0.01. Red and green colored circles correspond respectively to up- and down-regulated isogroups significant at both edgeR (P≤0.01) and MWW testing (P ≤ 0.05).