title: DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows.
abstract: 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.
authors.affiliation: DIANA-Lab, Biomedical Sciences Research Center Alexander Fleming, 16672 Vari, Greece. paraskevopoulou@fleming.gr
authors.forename: Maria D
authors.initials: MD
authors.lastname: Paraskevopoulou
authors.forename: Georgios
authors.initials: G
authors.lastname: Georgakilas
authors.forename: Nikos
authors.initials: N
authors.lastname: Kostoulas
authors.forename: Ioannis S
authors.initials: IS
authors.lastname: Vlachos
authors.forename: Thanasis
authors.initials: T
authors.lastname: Vergoulis
authors.forename: Martin
authors.initials: M
authors.lastname: Reczko
authors.forename: Christos
authors.initials: C
authors.lastname: Filippidis
authors.forename: Theodore
authors.initials: T
authors.lastname: Dalamagas
authors.forename: A G
authors.initials: AG
authors.lastname: Hatzigeorgiou
mesh_terms: D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D034622:RNA Interference; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012984:Software; D018511:Systems Integration; D057188:Workflow
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger