Question: which form of miRNA corresponding to TCGA?
2
gravatar for a511512345
19 months ago by
a51151234580
China guangxi nanning
a51151234580 wrote:

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
mirnas • 831 views
ADD COMMENTlink modified 18 months ago by gaoteng10 • written 19 months ago by a51151234580
1
gravatar for gaoteng
18 months ago by
gaoteng10
gaoteng10 wrote:

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!

ADD COMMENTlink written 18 months ago by gaoteng10
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