which form of miRNA corresponding to TCGA?

Question

[a511512345]

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

Answer 1

[gaoteng]

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!

[Nobody]

Hi! could you explain to us how you did to have two files.