I have conserved and novel miRNAs of my plant samples and done the target prediction. Can any one please suggest me how could or any computational tools for analyzing the miRNA regulating pathways?
Dear Nadiya
If you do pathway enrichment for any microRNA/miRNA family target genes, you may obtain a view on the patjhways whcih regulate by a given microRNA.
For pathway enrichment the DAVID (https://david.ncifcrf.gov/summary.jsp) is my favorite. I think the website worth a try.
Cheers,
Hamid
IPA has miRNA pathway analysis but I am not sure if it include plant model. Do you have the miRNA expression data? Or you just want to look at which pathways are enriched as regulated by these miRNAs? I think miRNA target prediction is more straightforward in plants. If you already did the target prediction, you can use BLAST2 GO to do GO enrichment analysis.
Thank you Hamid, Let me check with DAVID.
Thank you Shuai chen. I have my miRNA expression data.Let me try with your suggestion.
Dear Nadiya
in my analyses I used Genemania for enrichment annotatiotion of target genes for a specific miRNA. In the "Function" table of the window you could see which cellular processes are linked with the target genes you submitted to the tool. I also suggest you to take a look at Kegg which is a universal tool for these purposes.
Regards
Thankyou Filippo for this good suggestion, I tried Genemania its working good.
Hi Nadiya
Be careful about indirect approaches which can be very sensitive to biases and lead you to wrong conclusions. We did not provide any tool but guidelines to perform such pathway analyses starting from microRNA: http://nar.oxfordjournals.org/content/43/7/3490
I hope it will be helpful
I don't think there is a specific enrichment annotation for miRNA pathway. If anyone knows, please share.
Since you've done the target prediction, you can basically use any gene enrichment annotation tool. One that hasn't been mentioned is ToppGene. Note the two p!
Thank you Patrice, your article seems really useful.
Thank you Cenny
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