Why microRNA MiRBase ID in TCGA and Target scan does not match with each other well ?

[watermark]

Hi all,

I downloaed miRNA-seq data from TCGA. I looked at miRNA ids and they are miRBase IDs. also I'm processing TargetScan data set. I looked at the IDs in miR_Family_Info.txt from TargetScan. for some of the miRBase IDs from TCGA, there is no match in miR_Family_Info.txt. what should I do to solve this problem ?
as example :
in TCGA we have :
miRNA_ID

hsa-let-7a-1
hsa-let-7a-2
hsa-let-7a-3

But in TargetScan we have only :

hsa-let-7a

Does someone suggest me solution? I have to use TargetScan and TCGA.but the problem is this ID mapping. some some IDs in TCGA, there is no match in TargetScan.

[TiborNagy]

The hsa-let-7a-1 is a hairpin ID, but the mature miRNA sequences are the same. Maybe simply omit the last digit won't cause trouble.

[watermark]

There is two problem here :

all miRNAs in TargetScan are in mature form, which in the name of all of them there the R is capital; like hsa-miR-103a. but in TCGA, all miRNAs are in the form of miRNA precursor ( the lack of capitalisation of “mir” tells us we’re talking about the miRNA precursor); hsa-mir-103a

now the question is that, is the expression level of miRNA precursor equal to mature miRNA expression level in cell ?

Can I map miRNA precursor to mature miRNA ?

[peterawe]

Most hairpin/precursors will yield two mature miRNAs (5p and 3p), in this case let-7a-5p and let-7a-3p. TCGA just adds these numbers together and give you a summed count over the hairpin. The 5p and 3p have however very different sequences and thus targets different transcripts. You do need the expression of each arm, without it your results may be less than informative. TCGA has mede these data available but in a much less accesible form: https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp

[watermark]

Can you be more clear about :

1) Is the expression value of miRNA precursore is equivalent to it's corresponding mature miRNA form ?
for example in targetscan I have: hsa-miR-18a but in TCGA I have : hsa-mir-18a (smal 'r' in miR represent miRNA precursore)
2) What should I do with the miRNA which represent the stem loop ?
for example: in TCGA I have cases like :
hsa-mir-92a-1
hsa-mir-92a-2 wich they call it : Stem-loop sequence hsa-mir-92a-1 in miRBase database

but in TargetScan I have:
hsa-miR-92a

[peterawe]

Can you be more clear about :

1) Is the expression value of miRNA precursore is equivalent to it's corresponding mature miRNA form ?
for example in targetscan I have: hsa-miR-18a but in TCGA I have : hsa-mir-18a (smal 'r' in miR represent miRNA precursore)
2) What should I do with the miRNA which represent the stem loop ?
for example: in TCGA I have cases like :
hsa-mir-92a-1
hsa-mir-92a-2 wich they call it : Stem-loop sequence hsa-mir-92a-1 in miRBase database

but in TargetScan I have:
hsa-miR-92a

1. No; the precursor expression is the sum of both arms, all reads aligned to the hairpin. If you have a look at http://www.mirbase.org/cgi-bin/mirna...?acc=MI0000072 and the "Deep Sequencing" frame you see a quite typical example.

In this case, the hairpin precursor expression is approximately equal to 18a-5p.

2. This miRNA is encoded twice in the genome. Therefore most of the short sequencing reads will align equally good to the two loci. It will be just as good/bad using either one.

You are not the first or the last being frustrated by these issues...