We are trying to find the biological correlation between miRNA and certain genes. We found the general correlation through IPA (Ingenuity Pathway Analysis).
Thank you for your inputs!
I am not sure whether this will help with your question, but if you are trying to find novel interaction between miRNA and its target genes, there's a research that my supervisor did to identify relevant miRNA regulation for miRNA-driven subtypes of osteosarcoma (Camila M. Lopes-Ramos et al. Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. 2018).
You can find the network reconstruction method they used here (https://github.com/mararie/PUMA). Basically, the method is trying to find agreement between protein-protein interaction, transcription factor regulatory network and co-expression network.
There are also some network reconstruction methods such as iRafNet (Petralia F et al. Integrative random forest for gene regulatory network inference. 2015) that also have the potential to model miRNA regulation.
Hopefully this information help you with your research!
A classical approach is evalute in culture cells the level of the target gene by a construct with reporter along with the miRNA in cotransfection. Phisiologically you can assess the levels of the specific miRNA and target mRNA in different conditions of the animal, tissue, cell...along with the levels of the corresponding protein. See as example:
Brieño-Enríquez M. A., et al. “Exposure to endocrine disruptor induces transgenerational epigenetic deregulation of microRNAs in primordial germ cells” PLoS ONE 10(4): e0124296. doi:10.1371/journal.pone.0124296 (2015).
To check the correlation between
specific miRNAs and various expected genes. Simple way is to order microRNa mimics of your selected microRNAs and transfect them into the cells. After that, if the no. Of target genes suppose 1-10 u Check the effect on these genes after transfection of microRNA mimics by doing qRT-PCR and western blotting for target genes mRNA and protein levels or if the no. Of target genes is high design a MicroArray for these target genes in microRNA mimics transfected group compare that to in transfected group..
Dear Rajesh Pal
- Other members have already gave good answers
- miRNA functions is to target mRNA, my suggestion is, to use these two target prediction tools and see the miRNA-mRNA target binding relation (https://mirmap.ezlab.org/app/) & ( http://mirsystem.cgm.ntu.edu.tw/)
- Tools will help you to choose key genes target of your interested miRNA and then as following the methods suggested by other members (say overexpression, reporter assay), you can establish correlation
-I followed like this..
In addition to the previous answers, you may try the MIR tool of Broad Institute that report sets of target genes with short sequence motifs for each miR.
http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=MIR
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