Hello all , what is the best approach for miRNA and predicted target gene (without expression data) interaction networks analysis?
Hello all , what is the best approach for miRNA and predicted target gene (without expression data) interaction networks analysis?
Diana-microT 3.0 (miTG score ≧ 20 ) http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microtv4/index
TargetScan 5.1 = http://www.targetscan.org
PicTar = http://pictar.mdc-berlin.de/
miRanda = http://www.microrna.org
miRNet = http://www.mirnet.ca/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5085744/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990499/
http://onlinelibrary.wiley.com/doi/10.1002/wrna.1321/pdf
Hello Sam,
i suppose you mean for a group of target genes, search for known miRNA regulators or infer novel predictions. DIANA is a nice place to start from my personal experience:
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=site/page&view=software http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=taverna/index
Best,
Efstathios
For a quick run, try miRDB http://www.mirdb.org/, but the choise is somewhat arbitary and up to you. Take a look also to the following review, it looks interesting:
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For each of the tools mention above, except miRNet, I found they do not allow multiple queries at a time. miRNet seems to be good to retrieve interactions from a list of miRNAs/genes. Are there any other alternative tools that allow batch query?