I know there are several databases where one can look for the miRNA targets. But does anybody know if there is any database or online tool to identify putative miRNAs against a given gene of interest? I mean lets say I have a gene 'A' and I want to know what all known miRNAs could putatively target that particular gene. Any other suggestions are also welcome!
Thanks and Regards,
Ashraf
Hi,
You can use miRWalk database (mirwalk.uni-hd.de/) for this task. Moreover, this database also offers a comparative platform for the comparison of putative miRNA binding sites resulting from 10 different prediction data sets.
Step1: Choose "Gene Targets" option under the "Predicted Targets".
Step2: Select specie of interest (current human, mouse and rat) and paste your genes/entrezids of interest.
Step3: Choose regions of interest of genes.
Step4: Enter seed length and/or pvalue
Step5 : Select other programs for comparative study and sumit.
I hope this helps!
Best wishes
Hi,
You can use miRWalk database (mirwalk.uni-hd.de/) for this task. Moreover, this database also offers a comparative platform for the comparison of putative miRNA binding sites resulting from 10 different prediction data sets.
Step1: Choose "Gene Targets" option under the "Predicted Targets".
Step2: Select specie of interest (current human, mouse and rat) and paste your genes/entrezids of interest.
Step3: Choose regions of interest of genes.
Step4: Enter seed length and/or pvalue
Step5 : Select other programs for comparative study and sumit.
I hope this helps!
Best wishes
Hello
you can use target scan for human or other organism(http://www.targetscan.org/)
and also pictar ( http://pictar.mdc-berlin.de/ ) and also miRDB (http://mirdb.org/miRDB/) and also (microRNA.org ) and ( Microinspector).
good luck
all databases can do this..like if you go to miranda, target scan etc, their are options on main page whether you want to search miRNA or target gene!
Hi Ashraf
I hope not to be too late... I agree with the Mirwalk, but also I would like to recommend the miRecords tool (http://mirecords.biolead.org/)... It will also use many software for target prediction and will show all the results together, so you can decide.
You have many other tools compiled in my web site miRNAtools. Let me know if it is useful. Cheers and good luck.
https://sites.google.com/site/mirnatools/
Hi everybody,
All the answers are very useful and I highly appreciate the compilation of microRNA tools by Dr. Enguita.
Thanks to all.
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