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

Paraskevopoulou, Maria D.; Γεωργακίλας, Γεώργιος; Kostoulas, Nikos; Vlachos, Ioannis S.; Vergoulis, Thanasis; Reczko, Martin; Filippidis, Christos; Dalamagas, Theodore; Hatzigeorgiou, Artemis G.

doi:10.1093/nar/gkt393

Cited by 1,042 publications

(902 citation statements)

References 16 publications

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“…DIANA-MicroT tools are being developed in Artemis Hatzigeorgiou's laboratory for over a decade (Kiriakidou et al, 2004;Sethupathy et al, 2006;Megraw et al, 2007;Maragkakis et al, 2009;Alexiou et al, 2010;Maragkakis et al, 2011;Reczko et al, 2011;Vergoulis et al, 2012;Vlachos et al, 2012;Paraskevopoulou et al, 2013a;Paraskevopoulou et al, 2013b;Paraskevopoulou et al, 2016). MicroT is specifically trained on a positive and a negative set of miRNA binding sites located in 3'-UTR and CDS regions.…”

Section: Targetscan (Http://wwwtargetscanorg/vert_71/)mentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFS3

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This report is the outcome of an EFSA procurement aiming at investigating and summarising the state of knowledge on (I) the mode-of-action of dsRNA and miRNA pathways, (II) the potential for nontarget gene regulation by dsRNA-derived siRNAs or miRNAs, (III) the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing. The report is based on a comprehensive and systematic literature search, starting with the identification and retrieval of~190,000 publications related to the research area and further filtered down with keywords to produce focused collections used for subsequent screening of titles and abstracts. The report is comprised of an (I) Introduction to the field of small RNAs, (II) a Data and Methodologies section containing strategies used for literature search and study selection, and (III) the Results of the literature review organized according to the three main procurement tasks. The outcome of the first task reviews dsRNA and miRNA pathways in mammals (including humans), birds, fish, arthropods, annelids, molluscs, nematodes, and plants. Eight taxon-dedicated chapters are based on~1,400 cumulative references chosen from~10,000 inspected titles and abstracts. We review conserved and divergent aspects of small RNA pathways and dsRNA responses in animals and plants including structure and function of key proteins as well as four basic mechanisms: genome-encoded posttranscriptional regulations (miRNA), degradation of RNAs by short interfering RNA pools generated from long dsRNA (RNAi), transcriptional silencing, and sequence-independent responses to dsRNA. The outcome of the second task focuses on base pairing between small RNAs and their target RNAs and predictability of biological effects of small RNAs in animals and plants. The outcome of the last task reviews methodology, siRNA pools, and movement of small RNAs in plants. Potential transfer of small RNAs between species and circulating miRNAs in mammals is described in the final chapter.

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Section: Targetscan (Http://wwwtargetscanorg/vert_71/)mentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFS3

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“…Computational target prediction is coordinated in a sequence-speciic manner and the target genes are normally predicted based on information derived from the potency of binding between miRNA and putative targets. Generally, the methods for computational prediction of miRNA targets can be grouped in single platforms such as TargetScan [95], PicTar [115], RNAhybrid [105] or multiple platforms such as miRwalk [116], TarBases [121], miRecords [117] as well as integrative platforms which include downstream analyses of putative target genes such as DIANA-microT-CDS [96], miRPathDB [184], etc. A collection of tools for miRNA target prediction are available at htps://omictools.com/mirna-targetprediction-category and htps://tools4mirs.org/software/target_prediction/ [185] ( Table 3).…”

Section: Bioinformatics Tools For Target Prediction and Functional Inmentioning

confidence: 99%

“…Among the most popular integrated tools, DIANA-tools (www.microrna.gr) covers a wide scope and research scenarios integrating several tools such as DIANA-microT-CDS, DIANA-TarBase v7.0, DIANA-miRGen v3.0, DIANA-miRPath v3.0, and DIANA-mirExTra v2.0. DIANA-microT-CDS uses diferent thresholds and meta-analysis followed by pathway enrichment to perform miRNA target prediction [96]. DIANA-TarBase is a manually curated target database with more than half a million miRNA-target interactions curated from published experiments performed with 356 diferent cell types from 24 species.…”

Section: Integrated Tools For Mirna Analysismentioning

confidence: 99%

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Ngoc¹,

Dudemaine²,

Fomenky³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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The recent remarkable development of transcriptomics technologies, especially next generation sequencing technologies, allows deeper exploration of the hidden landscapes of complex traits and creates great opportunities to improve livestock productivity and welfare. Non-coding RNAs (ncRNAs), RNA molecules that are not translated into proteins, are key transcriptional regulators of health and production traits, thus, transcriptomics analyses of ncRNAs are important for a beter understanding of the regulatory architecture of livestock phenotypes. In this chapter, we present an overview of common frameworks for generating and processing RNA sequence data to obtain ncRNA transcripts. Then, we review common approaches for analyzing ncRNA transcriptome data and present current state of the art methods for identiication of ncRNAs and functional inference of identiied ncRNAs, with emphasis on tools for livestock species. We also discuss future challenges and perspectives for ncRNA transcriptome data analysis in livestock species.

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“…2) Service integration/composition [16], where authors provide road maps for breaking down large legacy business functions in to smaller pieces then creating services out of those in order to be integrated. Moving forward in this area, we see more shift towards understanding the importance of how we can use proven successful patterns to achieve a systematic modelling of entire systems built on services [17], and 3) Service engineering frameworks and processes [16], [18], [19], where they are advocating methodological (process oriented) approach to the whole processes of building new system entirely out of services (SOA). Table 1 summaries our compertive analysis between the SIE and the classical software engineering process described in many literature starting with Sommerville [20] and continued with many others literature [21], [22].…”

Section: Basic Business Servicementioning

confidence: 99%

Service Integration Engineering: A Paradigm Shift in Software Engineering

Sanati¹

2016

JSW

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Abstract:The engineering field has taken on many new disciplines as our scientific knowledge has grown. The latest discipline in this is software engineering. Service Oriented Architecture, and in a broader sense, Service Oriented Computing have influenced Information and Communication Technology towards a design of uncoupled yet coherent architectures of services. Hence, it would be fair to say that Service Oriented Computing is software development with services where existing services are composed and configured to create new composite services and applications. The basis for service composition is often a workflow, which is a logical sequence of activities that, together, model a coherent business process. As a result of that, a new engineering paradigm has been emerging from within the software development trend towards the Service Oriented Computing, which in this paper referred to as Service Integration Engineering. This paper is intends to identify distinctive attributes of such paradigm and the circumstances that may have been instrumental in giving rise to this new paradigm. We intend to establish whether the past and current trend towards building software applications or larger systems entirely from pre-defined building blocks calls service does in fact represent a paradigm shift in software engineering or it is just a temporary methodological shift to use certain pattern that would soon vanish with the emergence of other patterns.

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

Cited by 1,042 publications

References 16 publications

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Service Integration Engineering: A Paradigm Shift in Software Engineering

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