Fig. 1

Schematic illustration of differential transcript expression (DTE) and differential transcript usage (DTU) between conditions 1 and 2, for a gene with two isoforms. DTE implies that we can observe expression changes for at least one transcript between condition 1 and condition 2. However, the expression proportion of each transcript (as a percentage of the total expression of all transcripts of the same gene) does not necessarily change between conditions, and thus DTE does not necessarily imply DTU. In DTU, on the other hand, the relative expression of the isoforms of a gene changes between the conditions, whereas the total expression of the gene may or may not remain constant. Since at least one isoform must change expression in DTU, it also implies DTE. The numbers indicated on the transcripts in the figure represent expression levels (in arbitrary units) for easier interpretation. Note that in practice, many genes will have more than two isoforms, but the principal difference between DTE and DTU carries over