Question: Different miRNAs with same miRNA regions in TCGA
1
gravatar for Vasu
15 months ago by
Vasu510
Vasu510 wrote:

I have the miRNA data from TCGA as below: where for three miRNAs have the same mature miRNA region. Should I treat all of them as the same miRNA? I mean can I sum the read counts based on the miRNA region and treat all as single miRNA?

miRNA_ID    read_count  miRNA_region    barcode
hsa-let-7a-1    24  mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
hsa-let-7a-1    1   mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
hsa-let-7a-1    6   mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
hsa-let-7a-1 13634  mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
hsa-let-7a-2 41413  mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
hsa-let-7a-2    2   mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
hsa-let-7a-2    2   mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
hsa-let-7a-2    6   mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
hsa-let-7a-3    17  mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
hsa-let-7a-3    2   mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
hsa-let-7a-3    5   mature,MIMAT0000062 TCGA-3C-AALI-01A-11R-A41G-13
mirna mirnaseq tcga mirtarbase • 343 views
ADD COMMENTlink written 15 months ago by Vasu510

@Ian.Sudbery is away this week and may not be able to respond.

These three miRNA's have three separate entries (one, two, three) in miRBase. They are also on different chromosomes so you can consider that.

ADD REPLYlink written 15 months ago by GenoMax95k

In mirTarbase hsa-let-7a-5p is the only which has Accession MIMAT0000062. I actually want the names of the above table and miRNA target information names to be same. And this can be only based on miRNA_region. So, if I treat all the three miRNAs like that it will be same miRNA region for all those three. I don't think it is not possible for a biological analysis.

ADD REPLYlink written 15 months ago by Vasu510

I am not an miRNA expert so take the following with a grain of salt. If you are using miRNA_ID to do DE analysis then you would need to keep them separate. Hopefully someone else will chime in.

ADD REPLYlink written 15 months ago by GenoMax95k

Ok got the answer from this link miRNAseq isoform-to-mature miRNA quantification

ADD REPLYlink written 15 months ago by Vasu510
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