differential expression pattern of different isoforms of a gene

Question

[genesneuro]

Hi all..Has anyone came across situations where different isoforms of a gene are diferentially expressed (drastically) in an experiment..Is this biologically possible or is it an artefact

[GouthamAtla]

Its possible. Its quite commonly referred to as "Differential isoform/exon usage". It could also be isoform switching depending on condition.

[russhh]

is it a single exon that could be readily accounted for by read duplication?

Answer 1

[genesneuro]

the situation is like: when RNA-seq was performed for a gene knockout in a cell line v/s control, isoform-aa was up-regulated and Isoform-bb was down-regulated of ~50 genes. Majority of these isoforms differed by a single exon inclusion/exclusion. If this is biologically possible, how can we account these genes in a gene ontology/enrichment analysis?