Hi,
I'm new to this field, but need to generate a list of miRNAs that target (experimentally validated) a specific list of genes from my experiments. Preferably in batch mode, i.e. list of genes on input and list of miRNA on output. I understand that mirbase.org can do that for a reversed order: miRNA->gene.
Any links/comments will be much appreciated!
TarBase (http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index) is probably the most comprehensive database of experimentally validated miR target genes. You can search by miRNA or by target gene, and the type of experiment used for validation is listed so that you can assess the reliability of the predicted interaction. The citation for this database is an open-access publication in Nucleic Acids Research (PubMed ID 25416803).
Hi Dmitry,
In addition to the link provided above, i will like to suggest that you also take a look at psRNATarget. This is also an online tool that enables you to identify miRNA and target gene interactions. It goes as far as to show whether cleavage of mRNA or inhibition of translation will occur.
I use it a lot and its being helpful.
Hi Dmitry,
I would definitely agree with Robert on this. psRNATarget (http://plantgrn.noble.org/psRNATarget/) is a very nice online program which will identify targets in batch format.
DOI for the article: doi: 10.1093/nar/gkr319
Hello Dmitri,
In addition to Jesse's suggestion, mirDB website allows you to perform the search for predicted targets both ways (miRNAs>target genes and target genes> miRNAs) in animal species. You can enter your list of target genes separated by commas, and restrict the search to a given species. And the output is nicely complete, with miRNA name, GeneID, Gene name and description.
http://mirdb.org/miRDB/mining.html
Hope this is useful too :-)
Best regards
Sandrine
Definitely, I will use its multiple entries functionality, but concerned that it only provides predicted, not experimentally validated, miRs. But still thanks a lot, Sandrine.
I came across another database that's really nice - http://mirtarbase.mbc.nctu.edu.tw/index.php
It provides only validated miRNA-mRNA connections, lists the method of validation, and indicates whether the evidence is strong or weak. I'm not sure if the data differs from the other links provided, but the user interface is nice.
Jesse
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