Systematic bias at the gene level. (A) Schematic view of the CAGE platforms. Blue box indicates RNA; pink box, DNA; yellow box, EcoP15I sites; red box, internal EcoP15I sites; and green and purple boxes, 5′ and 3′ linkers. Text in blue suggests potential causes of gene quantification bias. (B) Relative expression of the CAGE profiles against RNA-seq quantification, according to GC content within 500 bp from RefSeq TSS. (C) Relative expression of the CAGE profiles depending on the presence of EcoP15I sites on an antisense strand to the gene orientation. (D) Relative expression of the RNA-seq profiles against HeliScopeCAGE quantification, according to GC content of the exons.
