DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows

By Maria D. Paraskevopoulou, G. Georgakilas, Nikos Kostoulas, Ioannis S. Vlachos, Thanasis Vergoulis, Martin Reczko, Christos Filippidis, Theodore Dalamagas, Artemis G. Hatzigeorgiou. Nucleic Acids Res., 2013

1,091 citations recorded by the source corpus.

MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA–gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1c458fd14cbd041d56cf6d85c66e53ef719a0f86

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Citations in the corpus

DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions (2017, methodology): “The database is also seamlessly interconnected with other available DIANA-tools, including microT-CDS (27) for in silico identification of miRNA targets, LncBase v2.”
miRBase: from microRNA sequences to function (2018, background): “For example, TargetScan (14), DIANA-microT (15) and miRDB (16) are amongst many resources that provide web interfaces to search and view the predicted target sites of most microRNAs.”
Tools for Sequence-Based miRNA Target Prediction: What to Choose? (2016, methodology): “0) the algorithm was improved (DIANA-microTCDS) [66] and the web server was completely redesigned [98].”
DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions (2014, neutral): “0 (28), microT-CDS (29) and LncBase (30), respectively.”
DIANA-miRPath v3.0: deciphering microRNA function with experimental support (2015, methodology): “Users can restrain the interactions and statistics only to an expressed genes subset which can be uploaded using the optional Expressed genes filter menu [3].”