I have the miRNA and it's regulatroy target information from TargetScan. all the miRNA IDs (miRBase IDs) from there are belong to mature miRNA form.
For my analysis I need also include the expresion levels of these miRNAs. I'm using TCGA data, but the problem is that, all miRNA IDs in TCGA data samples from RNASeq are for miRNA precursor.
now my questions are :
1) Is the expression value of miRNA precursore is equivalent to it's corresponding mature miRNA form ?
2) What should I do with the miRNA which represent the stem loop ?
For example in TargetScan I have ;
but in TCGA miRNA expression file I have :
hsa-mir-18a : precursore
hsa-mir-18a-1 : stem loop
hsa-mir-18a-2 : stem loop
basically miRNA IDs without capital R in it represent miRNA precursore.
We can go further — the (lack of) capitalisation of “mir” tells us we’re talking about the miRNA precursor (here)