Figure 1

Effect of differential alternative splicing on gene counts. In this toy example a gene with two isoforms is considered. Observing only the exon counts it may be reasonable to assume that sample one and two only contain transcripts from isoform one, while sample three only contains transcripts from isoform two. If the expression of a gene is measured as the sum of its exon counts then here sample three would generally be considered as differentially expressed from sample one or two. However, if this gene’s expression were measured only using the counts from the first exon, this gene would not be considered differentially expressed. It would be reasonable to assume that samples one, two and three all contain a similar number of transcripts for this gene.