Dear experts,
I have a list of miRNA and corresponding target genes for which i want to construct pathways and network interaction, so can you please suggest me any tool or software which will allow me to construct pathways using my selected miRNA and genes?
Yeah i used many algorithms, constructed pathways manually and published also, but now i am looking for automatic tool which allow users for large number of miRNA with there corresponding gene, and perform curated networking.
Thanks for your feedback.
Hi Pradeep,
first you should take a look at one miR database to ensure that your your miR target your selected genes (try http://www.mirbase.org). once you checked everything's well, or you try IPA (ingenuity) if you have a licence, or free counterparts as DAVID (https://david.ncifcrf.gov) to perform your analysis.
fred
Hi,
I suggest to build a proper miRNA target based resource for your own need. IPA is expensive and it has it's cons, but you can make the similar results with free databases as well, but it can be a bit time consuming.
Step 1. Find a database for miRNA targets - it depends on your preferences how sure you want to be at that the miRNA-target gene interaction is exist. Experimentally verified: Tarbase (http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index), miTarbase (http://mirtarbase.mbc.nctu.edu.tw/php/index.php)
Predicted: TargetScan (http://www.targetscan.org), the MIRANDa algorithm using mciroRNA.org (http://34.236.212.39/microrna/home.do)
Step 2. Use the affected genes and bind them to pathway ontologies I prefer GO for it. Simplest tool for enrichment is GOrilla (http://cbl-gorilla.cs.technion.ac.il/), but DAVID is good as well. You have to check your background.
You can write a proper hypergeometric test in R or in python as well using UNIPROT GO annotation or the Broad institution MolSIgDB annotation (http://software.broadinstitute.org/gsea/msigdb).
Alternatively you can use a PPI/gene network to bind to your miRNAs and you can see e.g. which genes are interacting with each other. Possibly your miRNA there are more effective in that path.
For signalling Omnipath (http://omnipathdb.org/), Signor (http://signor.uniroma2.it/) , Rectome (https://reactome.org/), SignaLink (http://signalink.org/).
PPI and other: STRING (https://string-db.org/) , BIOGRID (https://thebiogrid.org/), IntAct (https://www.ebi.ac.uk/intact/) HAPPI 2 (http://discovery.informatics.uab.edu/HAPPI/) etc. Check the confidence of each data sources.
Reactome BIOGRID and Omnipath has clients, but I usually manually build each databases at my own computer and work with them as an iGRAPH object, but this is my perversion.
Step 3. Running a random walker around the network to find the affected nodes and then do a GSEA or a GO analysis on them. Do it only if you do not see anything from the previous step.
Cheers,
Dezso
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