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      • Record: found
      • Abstract: found
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      Is Open Access

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

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          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.

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          • Record: found
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          Ensembl 2012

          Paul Flicek, M. Amode, Daniel Barrell … (2011)
          The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.
          Article 0 comments Cited 465 times – based on 0 reviews     Review now
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            MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation.

            Yvonne Tay, Jinqiu Zhang, Andrew M. Thomson … (2008)
            MicroRNAs (miRNAs) are short RNAs that direct messenger RNA degradation or disrupt mRNA translation in a sequence-dependent manner. For more than a decade, attempts to study the interaction of miRNAs with their targets were confined to the 3' untranslated regions of mRNAs, fuelling an underlying assumption that these regions are the principal recipients of miRNA activity. Here we focus on the mouse Nanog, Oct4 (also known as Pou5f1) and Sox2 genes and demonstrate the existence of many naturally occurring miRNA targets in their amino acid coding sequence (CDS). Some of the mouse targets analysed do not contain the miRNA seed, whereas others span exon-exon junctions or are not conserved in the human and rhesus genomes. miR-134, miR-296 and miR-470, upregulated on retinoic-acid-induced differentiation of mouse embryonic stem cells, target the CDS of each transcription factor in various combinations, leading to transcriptional and morphological changes characteristic of differentiating mouse embryonic stem cells, and resulting in a new phenotype. Silent mutations at the predicted targets abolish miRNA activity, prevent the downregulation of the corresponding genes and delay the induced phenotype. Our findings demonstrate the abundance of CDS-located miRNA targets, some of which can be species-specific, and support an augmented model whereby animal miRNAs exercise their control on mRNAs through targets that can reside beyond the 3' untranslated region.
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              • Record: found
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              Is Open Access

              TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

              Thanasis Vergoulis, Ioannis S Vlachos, Panagiotis Alexiou … (2011)
              As the relevant literature and the number of experiments increase at a super linear rate, databases that curate and collect experimentally verified microRNA (miRNA) targets have gradually emerged. These databases attempt to provide efficient access to this wealth of experimental data, which is scattered in thousands of manuscripts. Aim of TarBase 6.0 (http://www.microrna.gr/tarbase) is to face this challenge by providing a significant increase of available miRNA targets derived from all contemporary experimental techniques (gene specific and high-throughput), while incorporating a powerful set of tools in a user-friendly interface. TarBase 6.0 hosts detailed information for each miRNA–gene interaction, ranging from miRNA- and gene-related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. All database entries are enriched with function-related data, as well as general information derived from external databases such as UniProt, Ensembl and RefSeq. DIANA microT miRNA target prediction scores and the relevant prediction details are available for each interaction. TarBase 6.0 hosts the largest collection of manually curated experimentally validated miRNA–gene interactions (more than 65 000 targets), presenting a 16.5–175-fold increase over other available manually curated databases.
              Article 0 comments Cited 258 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): July 2013
                Publication date (Electronic): 16 May 2013
                Publication date PMC-release: 16 May 2013
                Volume: 41
                Issue: Web Server issue
                Pages: W169-W173
                Affiliations
                1DIANA-Lab, Biomedical Sciences Research Center ‘Alexander Fleming’, 16672 Vari, Greece, 2Department of Computer and Communication Engineering, University of Thessaly, 382 21 Volos, Greece, 3IMIS Institute, ‘Athena’ Research Center, 11524 Athens, Greece, 4Laboratory for Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School of Athens, University of Athens, 11527 Athens, Greece and 5National Center for Scientific Research DEMOKRITOS, Institute of Nuclear and Particle Physics, 15310 Aghia Paraskevi, Greece
                Author notes
                *To whom correspondence should be addressed. Tel: +30 210 9656310 (ext. 190); Fax: +30 210 9653934; Email: hatzigeorgiou@ 123456fleming.gr
                Correspondence may also be addressed to Maria D. Paraskevopoulou. Tel: +30 210 9656310 (ext. 190); Fax: +30 210 9653934; Email: paraskevopoulou@ 123456fleming.gr

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

                Article
                Publisher ID: gkt393
                DOI: 10.1093/nar/gkt393
                PMC ID: 3692048
                PubMed ID: 23680784
                SO-VID: 0671906f-a835-4b05-8996-36e4a081fb3d
                Copyright © © The Author(s) 2013. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                Date received : 4 March 2013
                Date revision received : 15 April 2013
                Date accepted : 18 April 2013
                Page count
                Pages: 5
                Categories
                Subject: Articles
                Custom metadata
                cover-date 1 July 2013

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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