DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways

Vlachos, Ioannis S.; Kostoulas, Nikos; Vergoulis, Thanasis; Γεωργακίλας, Γεώργιος; Reczko, Martin; Maragkakis, Manolis; Paraskevopoulou, Maria D.; Prionidis, Kostantinos; Dalamagas, Theodore; Hatzigeorgiou, Artemis G.

doi:10.1093/nar/gks494

Cited by 486 publications

(442 citation statements)

References 30 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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“…Target genes of deregulated miRNAs were listed using DiANA-TarBase database v6.0, which include experimentally validated miRNA targets in the literature. To explore the potential function of the whole miRNAs and target genes signature, DiANA-mirPath, a web-based DNA intelligent Analysis (DiANA)-miRPath v2.0 was used (http:// www.microrna.gr/miRPathv2) to perform enrichment analysis of differentially expressed miRNA gene targets in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway (12). The pathways were obtained with a P-value <0.05 and gene count.…”

Section: Mirna Validation By Quantitative Real-time Pcr (Qrt-pcr)mentioning

confidence: 99%

Exosome-derived microRNAs contribute to prostate cancer chemoresistance

Yang

Guan

et al. 2016

International Journal of Oncology

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Abstract. Certain microRNAs (miRNAs) play a key role in cancer cell chemoresistance. However, the pleiotropic functions of exosome-derived miRNAs on developing chemoresistance remain unknown. In the present study, we aimed to construct potential networks of miRNAs, which derived from the exosome of chemoresistant prostate cancer (PCa) cells, with their known target genes using miRNA expression profiling and bioinformatic tools. Global miRNA expression profiles were measured by microarray. Twelve miRNAs were initially selected and validated by qRT-PCR. Known targets of deregulated miRNAs were utilized using DIANA-TarBase database v6.0. The incorporation of deregulated miRNAs and target genes into KEGG pathways were utilized using DIANA-mirPath software. To construct potential miRNA regulatory networks, the overlapping parts of miRNAs and their targer genes from the selected KEGG pathway 'PCa progression (hsa05215)' were visualized by Cytoscape software. We identified 29 deregulated miRNAs, including 19 upregulated and 10 downregulated, in exosome samples derived from two kinds of paclitaxel resistance PCa cells (PC3-TXR and DU145-TXR) compared with their parental cells (PC3 and DU145). The enrichment results of deregulated miRNAs and known target genes showed that a few pathways were correlated with several critical cell signaling pathways. We found that hub hsa-miR3176, -141-3p, -5004-5p, -16-5p, -3915, -488-3p, -23c, -3673 and -3654 were potential targets to hub gene androgen receptor (AR) and phosphatase and tensin homolog (PTEN). Hub gene T-cell factors/lymphoid enhancer-binding factors 4 (TCF4) target genes were mainly regulated by hub hsa-miR-32-5, -141-3p, -606, -381 and -429. These results may provide a linkage between PCa chemoresistance and exosome regulatory networks and thus lead us to propose that AR, PTEN and TCF4 genes may be the important genes which are regulated by exosome miRNAs in chemoresistance cancer cells.

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“…For microT-CDS, a microT prediction threshold of >0.8 was set. DIANA-miRPath was used to perform functional annotation clustering and pathway enrichment analysis of multiple miRNA target genes (44). Two-sided Fisher's exact test and the X 2 test were used to classify the Gene Ontology (GO) category and KEGG pathway enrichment, and the FDR was calculated to correct P values.…”

Section: Methodsmentioning

confidence: 99%

Circulating microRNA signature for the diagnosis of very high-risk prostate cancer

Alhasan

Scott

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

125

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We report the identification of a molecular signature using the Scano-miR profiling platform based on the differential expression of circulating microRNAs (miRNA, miR) in serum samples specific to patients with very high-risk (VHR) prostate cancer (PCa). Five miRNA PCa biomarkers (miR-200c, miR-605, miR-135a*, miR-433, and miR-106a) were identified as useful for differentiating indolent and aggressive forms of PCa. All patients with VHR PCa in the study had elevated serum levels of miR-200c. Circulating miR-433, which was differentially expressed in patients with VHR versus low-risk (LR) forms of PCa, was not detectable by quantitative real-time PCR in samples from healthy volunteers. In blind studies, the five miRNA PCa biomarkers were able to differentiate patients with VHR PCas from those with LR forms as well as healthy individuals with at least 89% accuracy. Biological pathway analysis showed the predictive capability of these miRNA biomarkers for the diagnosis and prognosis of VHR aggressive PCa.

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DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways

Cited by 486 publications

References 30 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

Exosome-derived microRNAs contribute to prostate cancer chemoresistance

Circulating microRNA signature for the diagnosis of very high-risk prostate cancer

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