How to construct networking pathway using own miRNA with pre selected genes?

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

Abhishek Kumar

Did you try Ingenuity

and

alternatively use gene only network.

Pradeep Jaswani

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.

Frederic Lepretre

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

How to identify microRNA binding location in particular gene?

Is there any insilico tool available for pathway analysis??

Does anybody have ePath 3D software?

Which cell lines in prostate,breast and pancreatic cancer contain wild type P53?

How to overcome from a fungus contamination in a cell culture?

Is there a database available which contains data on miRNA-targeted genes in specific diseases with the validated gene on that particular organ?

MiRNA qpcr problem?

Can MicroRNA cross the blood brain barrier?

How to visualise pathways from a phosphoproteomics dataset?

Are exogenous molecules transferred between human cells during doubling ?

Has anyone encountered any problems with abm good microRNA primers for quantification of mature miRNAs?

What is the best way to fix plasma derived miRNA for subsequent cDNA synthesis?

What is the general miRNA yield one gets from the Qiagen miRNEASY serum/plasma advanced kit?

Which miRNA arm is a right target for analysis, 3p or 5p?

Is negative controls necessary for western blotting?

Can I predict miRNA by knowing the mRNA target?