3 months ago by
The levels of a given transcript can be regulated by several different processes. Some of these processes (such as transcript initiation) are shared between transcripts, but others (such as splicing and RNA stability) are not.
Sometimes transcript expression is entirely correlated across a gene: If you have two transcripts from the same promoter and that promoter is upregulated, you will see an increase in the levels of both transcripts.
Sometimes levels of transcripts within a gene are completely independent: If two transcripts from the same gene are transcribed from different promoters, and one of those promoters is upregulated, then the levels of one transcript will go up, and the other will stay the same.
And sometimes the levels of transcripts within a gene are exactly anti-correlated. If you have two transcripts from the same promoter, but are alternatively spliced, a change in splicing will necessarily involve an increase in the quantity of one transcript and a matching decrease in quantity of another.
In short, if you are interested in transcript levels, then don't talk about genes, where as if you are interested in talking about gene activity, then do gene level analysis rather than transcript level analysis.