metamaden/primir

Database of pairwise consensuses for miR-mRNA target interactions

PrImiR

Description

Database of pairwise consensuses for computationally predicted miR-mRNA target interactions.

Background

This package is downloadable using the following in R: require(devtools); install_github("metamaden/PrImiR")

The science of miR target prediction is actively evolving. There is no universal consensus for all computationally predicted miR-mRNA target interactions, and in addition most computationally predicted interactions have not been validated in the wet lab.

To mitigate the limitations of individual computational algorithms, this package provides a database of consensus predicted miRs (mature miRNAs) and miR-mRNA target interactions (present in at least two databases) using the latest available versions of five established and widely used miRNA databases and target prediction algorithms:

1. Target Scan (v.7.1)
2. Miranda/mirSVR (update 2010-08)
3. miRDB (v.5.0)
4. miRTarBase (v.6.1)
5. miRmap (update 2013-01-09)

1. Database Consensus Visualization: Simple Heatmap of random subset (N=2k miR-mRNA interactions) of PrImiR pairwise consensus miR-mRNA interactions database, showing presence of miR-mRNA interactions (rows) across databases (columns). blue=0/not present; red=1/present

2. Interactions (miR-mRNA targets) Predicted across databases

3. Scripts for Assembling And Annotating miRNA/miR Database

Check scripts folder for information. Check data folder for database and annotation files, including CpGs overlapping putative promoter regions (+/- 1KB from hairpin start site).

Citations

Agarwal, Vikram, George W Bell, Jin-Wu Nam, David P Bartel. Predicting effective microRNA target sites in mammalian mRNAs. eLife 2015;4:e05005

Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res. 2008 Jan; 36(Database Issue): D149-53.

Chou CH, Chang NW, Shrestha S, et. al. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. (2016) Nucleic acids research.

Vejnar, Charles E. and Evgeny M. Zdobnov. miRmap: Comprehensive prediction of microRNA target repression strength. Nucleic Acids Research 2012 Dec 1;40(22):11673-83. doi: 10.1093/nar/gks901

Wang, Xiaowei Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-Ligation studies. 2016 Bioinformatics. 32(9):1316-1322.

Wong, Nathan and Xiaowei Wang. miRDB: an online resource for microRNA target prediction and functional annotations. 2015 Nucleic Acids Research. 43(D1):D146-152.