Question

DB or Tool searching for miRNA validated targets in cancer?

0

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5.6 years ago

NT ▴ 20

Hi all, I have a list of miRNA and i want to know its validated target in a cancer and the pathways in which implicated. I used miRTarBase and i know there is many web servers but I want to know if there an R package or a tool not complicated (for beginner) to find miRNA validated tagets and recently updated. Thank you

miRNA Validated targets cancer pathways targets • 1.2k views

ADD COMMENT • link updated 5.6 years ago by poyarkov.stanislav ▴ 40 • written 5.6 years ago by NT ▴ 20

score 2 · Answer 1 · 2018-09-10

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Entering edit mode

5.6 years ago

poyarkov.stanislav ▴ 40

Hi Nesrine, I recommend you to try this resource: https://www.onco.io/ You can find there upto-date mannualy curated mIR targets involved in cancer. ONCO.IO contains more then 5500 highly validated targets . ONCO.IO also contains other interactions TF-->miR, TF-->gene target and PPIs. Regards, Stas

ADD COMMENT • link 5.6 years ago by poyarkov.stanislav ▴ 40

score 0 · Answer 2 · 2018-09-02

I don't know about databases specifically for validated targets in a cancer setting; however, there are databases that store both in silico and validated target predictions, though I am not sure on the tissues used in these databases.

For in silico predictions, miRNAtap is a program that I have used to good effect; however, you may find its implementation difficult.

A: miRNA target genes prediction.
A: Identifying miRNA, RNA-binding sites in UTRs (also note the other answer that mentions miRBase)

If you want to make your life easier and just look up interactions (validated or predicted) in a GUI, then use miRWalk 2.0.

Kevin