I downloaded the expression matrix for the miRNA from http://gdac.broadinstitute.org/, as shown in the following figure. I would like to know whether the miRNA's name corresponds to miR-5p or miR-3p or miR precursor?
Hybridization REF TCGA-2J-AAB1-01A-11R-A41G-13
miRNA_ID read_count reads_per_million_miRNA_mapped cross-mapped
hsa-let-7a-1 47078 7919.023369 N
hsa-let-7a-2 94156 15838.04674 N
hsa-let-7a-3 47350 7964.776679 N
hsa-let-7b 154379 25968.19977 N
hsa-let-7c 21240 3572.795283 N
hsa-let-7d 2512 422.54528 N
hsa-mir-1258 8 1.345686 N
hsa-mir-125a 4171 701.606833 N
hsa-mir-125b-1 11452 1926.348945 N
hsa-mir-125b-2 167 28.091187 N
hsa-mir-126 11402 1917.93841 N
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According to miRBase, "Distinct precursor sequences and genomic loci that express identical mature sequences get names of the form hsa-mir-121-1 and hsa-mir-121-2". (http://www.mirbase.org/help/nomenclature.shtml) So let-7a-1, let-7a-2, and let-7a-3 are stemloop sequences.
I think to get the mature transcript expressions, you need to parse the data from TCGA miRNASeq isoform quantification files (ending with .mirbase21.isoforms.quantification.txt). Here is my script to do so: https://github.com/teng-gao/genomics_utils/blob/master/README.md#process-tcga-mirnaseq-isoform-quantifications
Please correct me if I'm wrong!
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