The effect of intronic expression on fold change calculation. A) Estimation of log2 FC considering exonic reads only (x-axis) compared to FC calculating counting exonic and intronic reads (y-axis). Red points represent genes called DE when using both counting schemes with the same direction of fold change, peach points represent the two genes that are called as DE with both schemes, but with opposite directions of fold change. Green points show genes called DE when considering exonic reads only, but not when considering exonic and intronic reads. Blue points show genes DE when considering exonic and intronic reads but not when considering exonic reads only. B) Distribution of the ratio of fold changes estimated by both methods. Calculated by subtracting the log2 FC values calculated using full gene expression from log2 FC calculated exon expression only. Ci, Cii) Genome graphs for gene St3gal6, showing intronic expression that is not proportional to exonic expression, i.e. that is increased following SNT. The figure comprises a series of “tracks” for each gene, and its expression levels for SNT samples (Ci) and naive samples (Cii). The top tracks show the genomic coordinates of the gene on chromosome 11 (precise position marked in red). The middle histogram-like tracks show the positions of RNA-seq reads mapping to the genomic location of the gene. Below these tracks is a track showing the gene structure (exons are represented by boxes, introns are represented by arrowed lines, the direction of these arrows shows the direction of transcription). Bottom track shows the position of the microarray probes that map to the genomic location of the gene.