This is a test version of Biostars. For the public version, visit https://www.biostars.org.
miRNA Target database?

Hi Everybody,

Somebody knows which is the most complete and updated database for looking miRNA gene-targets (validated targets)? I have tried miRWalk but some results makes me think that is incomplete or outdated. I have hundreds of miRNAs to assign function so I need that the data looks like GSEA files on miRwalk.

Thanks!

mirna mirna-seq target database
• 4,346 views • link
updated by zizigolu zizigolu • written by Buffo Buffo

You are looking for miRNA-mRNA pairs validated using experimental data? I expect that set to be rather limited.

• 0 views • link
written by WouterDeCoster WouterDeCoster

Yes, it is, but target prediction is even worst and limited I think so.

• 0 views • link
written by Buffo Buffo

5 answers

You may want to look at the list of 70 miRNA target prediction resources.

The ranking list includes various information about each database, such as:

  1. list of features
  2. list of organisms
  3. last update
  4. citations per year
  5. popularity
  6. paper & url
• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

Highly recommend miRTarBase - provides a variety of filtering options including validation status.

• 0 views • link
written by Khader Shameer Khader Shameer

Yes, for my research it was the best, and also it has the last update upon all others databases.

• 0 views • link
written by Buffo Buffo

Have a look at

1) TargetExpress

2) miRbase

3) miRcode

• 0 views • link
written by EagleEye EagleEye

You can try the starBase (http://starbase.sysu.edu.cn/) database, it has been updated to decode miRNA-mRNA, miRNA-lncRNA, miRNA-sncRNA, miRNA-circRNA, miRNA-pseudogene, protein-lncRNA inteactions from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) and degradome sequencing data.

starBase also decipher Pan-Cancer Analysis Networks of lncRNAs, miRNAs, ceRNAs and RNA-binding proteins (RBPs) by mining clinical and expression profiles of 14 cancer types (>6000 samples) from The Cancer Genome Atlas (TCGA) Data Portal.

• 0 views • link
written by lsp03yjh lsp03yjh

http://multimir.ucdenver.edu/

• 0 views • link
written by zizigolu zizigolu

Log in to answer this question.

More posts like this