Question: miRNA target genes prediction.
0
gravatar for anu014
2.2 years ago by
anu014170
India
anu014170 wrote:

Hello Biostars!

Today I'm trying a new pipeline for miRNA prediction. I used 'miRDeep' for miRNA prediction & after that I used 'DESeq' for differential analysis. Now I'm wondering how to get target genes for these miRNA. There're several packages such as targetscan.Hs.eg.db, multiMiR, miRNATarget etc. Which one do you all suggest?

And what all downstream analysis can be done related to miRNA ?

Please do suggest. Thanks you all :)

mirna R gene • 958 views
ADD COMMENTlink modified 2.2 years ago by lieven.sterck7.2k • written 2.2 years ago by anu014170
1
gravatar for Kevin Blighe
2.2 years ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

I have recently used miRNAtap, which produces an aggregate score from up to 6 mir target databases and ranks the predicted targeted genes.

This can then be used in conjunction with topGO and KEGGprofiler in order to perform gene enrichment and pathway analysis of the predicted target genes.

Further information, take a look here: A: Identifying miRNA, RNA-binding sites in UTRs

Kevin

ADD COMMENTlink written 2.2 years ago by Kevin Blighe56k

It's pretty cool. One of the best package I found today. Thank you.

But I am still not fully satisfied, its manual says : 'Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation)'.

Can it be customized for different species too, somehow?

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by anu014170

On which species are you working? It can be that the data you require simply does not yet exist.

ADD REPLYlink written 2.2 years ago by Kevin Blighe56k

Right now I'm doing testing on Human data. But I've to work on Danio rerio in few days..

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by anu014170
0
gravatar for lieven.sterck
2.2 years ago by
lieven.sterck7.2k
VIB, Ghent, Belgium
lieven.sterck7.2k wrote:

Its' not really an R package so not sure if this one can be of use : TAPIR

but it has a standalone version as well (see the manual pages)

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by lieven.sterck7.2k

It's nice one, but it's limited to plants only.. I wonder can we customize it for different organisms too.

ADD REPLYlink written 2.2 years ago by anu014170

Good question. should somehow be possible I guess but you probably will have to go into the code and change a few things, and of course you will need the appropriate info (eg. typical miRNA length etc) to customize it

ADD REPLYlink written 2.2 years ago by lieven.sterck7.2k
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