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It is important to distinguish differential transcript usage (DTU) from gene-level differential expression and from transcript-level differential expression (DTE). In particular, DTU considers changes in the proportions of the isoforms of a gene that are expressed as opposed to changes of the individual transcript levels. DTU implies DTE but not necessarily the reverse. Although the main transcriptional units of interest are the transcripts, it has been difficult to obtain accurate and precise transcript-level expression estimates due to the extensive overlap between different transcripts. This has prompted researchers to develop alternative ways of representing and analyzing the observed data. One such approach, which has been used as a surrogate for DTU, is differential exon usage (DEU), where data are represented on the level of disjoint counting bins.
Source: (Soneson et al., 2016) Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage. Genome Biol.