differential gene expression gene names/id vs transcript id

Question

[Jalil Sharif]

Is there a gold standard for volcano plots, I understand that differential gene expression, you want to know if genes are up or down regulated, however, in cases of interventional experiments, it is usually the underlying transcript that are differentially expressed, hence shouldn't transcripts' (with annotated gene names) be illustrated on volcano plots?

[ATpoint]

What are "interventional experiments" and why do you think (reference) you need transcripts rather than genes?

[ATpoint]

By the way, isoform analysis is much harder because of the mapping uncertainty. Many exons are shared between transcripts of the same gene, so the mapping is often ambiguous, and the DE testing needs to respect that. Multiple testing burden is also much higher. Transcript-wise analysis is not standard. My feeling is that 99.9% of DE analysis is gene level where we sum counts of transcripts per gene and do not go down that rabbithole of really looking at transcripts. For protein-coding genes there is often a dominant isoform, at least this is what the APPRIS paper was about.

Answer 1

[rfran010]

Displaying transcripts from all genes would make the volcano plot hard to read. And if a gene goes up, all those transcripts would go up as well and wouldn't necessarily inform you of the relative abundance of the isoforms. You could do it though and see.