miRNAs interaction networks analysis

Question

[Sam]

Hello all , what is the best approach for miRNA and predicted target gene (without expression data) interaction networks analysis?

Answer 1

[Leite]

To predict miRNA targets

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/

Articles:

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

miRNA function predict:

http://www.cuilab.cn/mirupnet

http://bnet.egr.vcu.edu/miRegulome/analysis.html

http://www.funcpred.com/

[Arindam Ghosh]

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?

Answer 2

[svlachavas]

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

[Sam]

DIANA-microT web server is under maintenance, could introduce any other?

[svlachavas]

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:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5187787/