I am investigating a gene, and on ensemble, it has multiple variants. How can i know which gene or protein isoform is most active?
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1$\begingroup$ Welcome to SE Biology. Please read the Help on asking good questions, and then take care to explain precisely what you mean, providing adequate context. You capitalized the wrong word in your title, and the one you did capitalize is ill chosen, as it suggests a comparison of their fundamental properties, whereas I imagine you are interested in the relative expression of the transcripts encoding the different protein isoforms. Depending on the organism, this may vary with tissue, developmental stage etc. But the simple answer is you can’t tell from Ensembl: you need to search the literature. $\endgroup$– DavidCommented May 16 at 16:46
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While David has a point that for specific genes you should look at in vivo data, significant amounts of work has been done to identify representative transcripts, often using direct experimental evidence.
One such effort is MANE-Select. When in doubt, or specifically when doing high-throughput or computational work, I would choose the MANE-Select transcript.
The idea behind it is to find a single transcript that is agreed upon by NCBI and ENSEMBL and to go through various steps of automated and manual curation to provide a "ground truth" expression product for a particular gene.
In vivo data includes techniques such as 5' RACE and CAGE to identify transcript coordinates that broadly agree with transcription starts and stops, among other steps.
Note: MANE-Select is only for human genes so far as I know.
