I am reading the literature "Link" and I have seen terminologies which are the following: Differential transcript expression (DTE) refers to change in one of the isoforms. Differential gene expression (DGE) refers to change in overall gene expression (i.e. expression as the sum of the expression of the two isoforms). Differential transcript usage (DTU) refers to change in relative expression between the two isoform. Gene differential expression (GDE) refers to change in expression along the red line. Note that DGE, DTU and DGE are special cases of GDE.
Now I want to know which isoform of some specific gene (lets say TGF-beta) is highly expressed and which one in less expressed in certain tissue. According to my understanding I need to do DTE analysis. if so what workflow should i use.