Hello everyone,

I have a list of 30 microRNAs  and I want to build a network of interaction with the targets.

Well, I'm thinking about use these databases:

1. [TargetScan Release 7.2][1]
2. [mirTarBase v6.0][2]
3. [enter link description here][3]
4. [microT-CDS 5][4]
5. [miRWalk 3][5]

And as a cut-off the target has to be present in 3 of these databases and have at least two microRNAs  as targets.

**First point:** Does this approach look robust?

**Second point**: miRWalk 3 seems to use other bases (miRBase, TargetScan and miRDB) as Resources for miRNA-target data [http://mirwalk.umm.uni-heidelberg.de/resources/][6] Am I right? If so, it seems redundant to use it here in my approach.

If anyone can give me some advice on how to do this analysis I will be very grateful, I have read several articles and each author does this analysis in a different way.


  [1]: http://www.targetscan.org/vert_72/
  [2]: http://mirtarbase.mbc.nctu.edu.tw/php/index.php
  [3]: http://www.mirdb.org/
  [4]: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=MicroT_CDS/index
  [5]: http://mirwalk.umm.uni-heidelberg.de/
  [6]: http://mirwalk.umm.uni-heidelberg.de/resources/
Yes, that's the conclusion that I got, too, i.e., that each author does it a different way. You know what? - I also did it a different way and here's what I did:

Given that most of these databases provide *in siico* predictions, and in some cases have come under scrutiny and criticism, the more corroborative evidence that you can accumulate for each mir, the better. There is an R package that does this for you, called <a href="https://bioconductor.org/packages/devel/bioc/vignettes/miRNAtap/inst/doc/miRNAtap.pdf">miRNAtap</a>. Whilst it doesn't have all of the databases that you mention, it does look at:

 - DIANA (Vlachos et al., 2012)
 - PicTar (Krek et al., 2015)
 - TargetScan (Agarwal et al., 2015)
 - miRanda (Betel et al., 2008)
 - miRDB (Wong & Wang, 2015)

The good thing here is that you can automate it and say that you want evidence for an interaction in at least 3 of these databases, or even 5 (all). *miRNAtap* also let's you to do gene enrichment of the genes targeted by each of your mirs of interest, whilst in addition the tutorial to which I've linked also shows how you can perform KEGG pathway enrichment of these, too (using *KEGGprofile*).

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miRWalk, I believe, was the database that came under some scrutiny in the past, but they appeared to then improve the data held in it. For one, they actually have validated mir-to-mir, mir-to-gene, etc interactions, i.e., from functional studies. In my study (yet to be published), I used miRWalk as a sort of secondary validation step for anything of interest found in the first part using *miRNAtap*.

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After you have identified some key mirs and gene targets, you can develop some nice figures like a *mirPrint* (a term that I chose) and a graph (yet unnamed) that shows the key mirs and their gene targets, and also the layering of the graph indicates how many mirs target the same gene.

<a href="https://imgbb.com/"><img src="https://image.ibb.co/mon7yy/sss.png" alt="sss" border="0"></a>


<a href="https://imgbb.com/"><img src="https://image.ibb.co/h36d5d/d.png" alt="d" border="0"></a>



Just to give you some ideas.


Kevin