Question: Tools For Mamalian Mirna Target Prediction
2
gravatar for biolab
6.8 years ago by
biolab1.2k
biolab1.2k wrote:

Hi everyone,

I am interested in mamalian miRNA target prediction. To my knowledge, the classical software for miRNA target prediction in mammales is Targetscan, which was developed by D.Bartel's lab (Cell, 2003). I would like to know the much recent progress in this field. Could anyone working in thisarea suggests me some recent tools ?

Thank you very much!

mirna • 2.3k views
ADD COMMENTlink modified 6.6 years ago by zhxq09140 • written 6.8 years ago by biolab1.2k
3
gravatar for Ashutosh Pandey
6.8 years ago by
Philadelphia
Ashutosh Pandey12k wrote:

Well there are dozens of tool available for that now. Just read some recent reviews:

http://bib.oxfordjournals.org/content/early/2012/11/22/bib.bbs075.full

http://www.nature.com/nrg/journal/v13/n4/full/nrg3162.html

http://www.mdpi.com/1422-0067/14/4/8179/pdf‎

http://journal.imbio.de/articles/pdf/jib-127.pdf‎

ADD COMMENTlink modified 6.4 years ago by Istvan Albert ♦♦ 84k • written 6.8 years ago by Ashutosh Pandey12k

Thanks, ashutoshmits. The links are really helpful!

ADD REPLYlink written 6.8 years ago by biolab1.2k
2
gravatar for Charles Warden
6.8 years ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

In general, my personal preference would be to use known associations rather than predicted associations: the lists of TargetScan targets can get pretty large.

If you have an institutional license, I think IPA provides the best tool for miRNA targets (both known and predicted). If you have mRNA data, it can also filter the list based upon mRNA and miRNA expression (which I think is really important, if you are working with predicted targets).

If you don't have an IPA license, I think TarBase is the next best thing (for known miRNA targets):

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index

ADD COMMENTlink written 6.8 years ago by Charles Warden7.9k
2
gravatar for zhxq09
6.6 years ago by
zhxq09140
China
zhxq09140 wrote:

Different miRNA target prediction programs produce different results and have high false positive rates. You can use CLIP-Seq datasets to further filter the predicted miRNA targets. starBase collect and curate 111 CLIP-Seq (PAR-CLIP, CLASH, HITS-CLIP, ICLIP) datasets.

You can download them at download page: http://starbase.sysu.edu.cn/download.php

ADD COMMENTlink written 6.6 years ago by zhxq09140
1
gravatar for Asaf
6.8 years ago by
Asaf8.4k
Israel
Asaf8.4k wrote:

You should consider these tools in the light of new data from the CLASH experiment. It turns out that most of the assumptions used for target predictions are not accurate.
A prediction tool with a different approach than the seed is RepTar. For some reason it was left aside in many discussions.

ADD COMMENTlink written 6.8 years ago by Asaf8.4k
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