Figure 8. Comparison of Gencode protein-coding genes RPKM and RPKUM expression values as measured in brain tissue (data from [19]).

Both axis are log-scaled, and each dot represents a protein-coding gene with or without annotated paralogous genes (in green and red, respectively). Protein coding genes totally or partially included in segmental duplications are presented in the top panel, whereas those not overlapping segmental duplications are shown in the bottom panel. The figure illustrates the importance of taking into account the mappability information in order not to underestimate expression level. Without mappability correction, two main reasons are shown to introduce a bias in the quantification of expression levels: gene having paralogs, and genes overlapping segmental duplications.