Is the canonical transcript usually the highest expressed isoform across tissues? If not, why—and how does this impact our conclusions and downstream resource design?
Has anyone quantified this in GTEx or other human datasets?
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Shicheng Guo
Is the canonical transcript usually the highest expressed isoform across tissues?
Canonical transcript selection is done using the criteria mentioned in this blog post from Ensembl --> https://www.ensembl.info/2021/04/16/update-to-the-ensembl-canonical-transcript-set/
While RNAseq data is used, it is just one of the criteria that contributes to a final score.
Although maybe we could say that it is not clear how/why a given selection was made.
Additional details are here --> http://www.ensembl.org/info/genome/genebuild/canonical.html?redirect=no
Interesting details, looks a little convoluted, but great to know there is a resource where it is all listed.
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