DIANA-miRPath v3.0 database has been extended to support features such as microRNA nomenclature history (18 ), a novel miRNA/gene name suggestion mechanism, as well as analysis support for seven species (H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, G. gallus and D. rerio). The new database schema incorporates KEGG pathways, as well as GO and GOSlim annotations, enabling functional annotation of miRNAs and miRNA combinations using all datasets, or their subsets (GO cellular component, biological processes or molecular function). Gene and miRNA annotations are derived from Ensembl (19 (link)) and miRBase (20 (link)), respectively. Single nucleotide polymorphism locations and pathogenicity are derived from dbSNP (21 (link)).
miRNA:gene interactions are derived from the in silico miRNA target prediction algorithms: DIANA-microT-CDS and TargetScan 6.2, the latter in both Context+ and Conservation modes. DIANA-microT-CDS is the fifth version of the microT algorithm (3 (link)). It is a highly accurate target prediction algorithm trained against CLIP-Seq datasets, enabling target prediction in 3′ UTR and CDS mRNA regions. The user of DIANA-miRPath v3.0 can also utilize experimentally supported interactions from DIANA-TarBase v.7.0. TarBase v7.0 incorporates more than half a million experimentally supported miRNA:gene interactions derived from hundreds of publications and more than 150 CLIP-Seq libraries (17 (link)). The number of indexed interactions is 9–250-fold higher compared to any other manually curated database. The user of miRPath v3.0 can harness this wealth of information and substitute or combine in silico predicted targets with high quality experimentally validated interactions. Currently, this functionality is supported for H. sapiens and M. musculus and C. elegans, since most relevant wet-lab experiments correspond to these species. As more experimental data become available for other organisms in DIANA-TarBase, the experimentally supported functional analysis module will be further extended.
miRNA:gene interactions are derived from the in silico miRNA target prediction algorithms: DIANA-microT-CDS and TargetScan 6.2, the latter in both Context+ and Conservation modes. DIANA-microT-CDS is the fifth version of the microT algorithm (3 (link)). It is a highly accurate target prediction algorithm trained against CLIP-Seq datasets, enabling target prediction in 3′ UTR and CDS mRNA regions. The user of DIANA-miRPath v3.0 can also utilize experimentally supported interactions from DIANA-TarBase v.7.0. TarBase v7.0 incorporates more than half a million experimentally supported miRNA:gene interactions derived from hundreds of publications and more than 150 CLIP-Seq libraries (17 (link)). The number of indexed interactions is 9–250-fold higher compared to any other manually curated database. The user of miRPath v3.0 can harness this wealth of information and substitute or combine in silico predicted targets with high quality experimentally validated interactions. Currently, this functionality is supported for H. sapiens and M. musculus and C. elegans, since most relevant wet-lab experiments correspond to these species. As more experimental data become available for other organisms in DIANA-TarBase, the experimentally supported functional analysis module will be further extended.
