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miRWalk2.0: a comprehensive atlas of microRNA-target interactions

Nature Methods volume 12, page 697 (2015)Cite this article

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miRWalk2.0 (http://zmf.umm.uni-heidelberg.de/mirwalk2) is a comprehensive archive, supplying the largest available collection of predicted and experimentally verified microRNA (miRNA)-target interactions (∼949 million), with novel and unique features that improve upon the previous version miRWalk1. miRWalk2.0 was developed to generate possible miRNA interactions with all the regions of a gene by gathering 13 prediction data sets from existing miRNA-target resources (Table 1, Supplementary Methods, Supplementary Fig. 1 and Supplementary Tables 1–3). The web interface of miRWalk2.0, which contains a predicted-target module and a validated-target module, hosts a multilayered view of data and offering information on miRNAs, genes, epigenomics, pathways, ontologies, protein classes, phenotype, genotype, single-nucleotide polymorphisms, functional networks, tandem mass spectra and relevant PubMed articles. Additionally, information on human homologous genes across 15 species can be downloaded to conduct an interspecies analysis. Notably, lists of genes or their identifiers can also be created for external tools such as the Database for Annotation, Visualization and Integrated Discovery (DAVID)2. Furthermore, miRWalk2.0 offers a framework to obtain statistically significant miRNA interactions on genes associated with pathways, ontologies, classes of gene and protein, disorders and mitochondrial genomes, and to explore pathways via the Kyoto Encyclopedia of Genes and Genomes (KEGG). Beyond prediction data, it also incorporates the experimentally verified information on miRNAs linked with genes, diseases, pathways, ontologies, cell lines and organs.

Table 1 Overview of information documented in miRWalk2.0
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  1. Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany

    Harsh Dweep & Norbert Gretz

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  1. Harsh Dweep
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  2. Norbert Gretz
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Correspondence to Harsh Dweep.

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Supplementary Figure 1, Supplementary Tables 1–3 and Supplementary Methods (PDF 945 kb)

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Dweep, H., Gretz, N. miRWalk2.0: a comprehensive atlas of microRNA-target interactions. Nat Methods 12, 697 (2015). https://doi.org/10.1038/nmeth.3485

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