What app is for "chemical->miRNA" and "chemical->mRNA"?

[이형삼]

I know that the stitch app is not an mRNA, but a database for viewing proteins.

Also, you need an app to view the mRNA targeted by miRNA.

Does the app I was talking about exist in Cytoscape? I didn't find it.

[Alex Pico]

You might want to look at CyTargetLinker. It leverages drugbank and mirTarBase to link chemicals to genes and miRNA to gene, and therefore chemicals to miRNA transitively. You can also create your own database files for the app if you know of a source for the interactions.

Follow website and tutorial links here:

http://apps.cytoscape.org/apps/cytargetlinker

 - Alex

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[이형삼]

I understood that it connects chemical to mRNA and miRNA to mRNA. However, it does not make sense to see chemicals as indirectly linking miRNAs. If chemical and miRNA target the same mRNA, isn't there a case where chemical directly targets mRNA without going through miRNA?

[Alex Pico]

By default, CyTargetLinker provides just a few database files. These do not happen to include chemical-miRNA integration (that I know of). If you can find a database that has those interactions, then you could attempt to build an xgmml file and add it to Cytoscape.

 - Alex

On Apr 27, 2020, at 9:37 PM, 이형삼 <hslee...@gmail.com> wrote:

I understood that it connects chemical to mRNA and miRNA to mRNA. However, it does not make sense to see chemicals as indirectly linking miRNAs. If chemical and miRNA target the same mRNA, isn't there a case where chemical directly targets mRNA without going through miRNA?

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[이형삼]

Thank you for answer.

If what I understand is correct, I understand that to see the relationship between chemical and miRNA, I need to find a database outside of cyTargetLinker and download the data from there and draw it directly without using cyTargetLinker. I'm very sorry, but did you mention the reason you mentioned XGMML format because when you download data from a public database, you can download it in XGMML format?