Question: which form of miRNA corresponding to TCGA?
4
gravatar for a511512345
3.4 years ago by
a511512345120
China guangxi nanning
a511512345120 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 • 1.5k views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 3.4 years ago by a511512345120
2
gravatar for gaoteng
3.2 years ago by
gaoteng70
gaoteng70 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 3.2 years ago by gaoteng70

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

ADD REPLYlink written 8 months ago by zak 0
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