DIANA-miRPath protocols

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DIANA-miRPath specifications

Information


Unique identifier OMICS_08479
Name DIANA-miRPath
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio

Maintainer


  • person_outline Artemis G. Hatzigeorgiou <>

Publications for DIANA-miRPath

DIANA-miRPath in pipelines

 (9)
2018
PMCID: 5844946
PMID: 29523845
DOI: 10.1038/s41598-018-22701-2

[…] expression levels intra- and inter-conditions, and it applies the t test (instead of the wald test)., potential mirna-targeted genes and their impact on the biological pathways were assessed using diana-mirpath v2.0 (http://diana.imis.athena-innovation.gr)., 1 µg and 4 µg of total hippocampal rna were used in the reverse transcription reaction (rt) for coding and non-coding rna expression […]

2018
PMCID: 5929417
PMID: 29731974
DOI: 10.18632/oncotarget.24800

[…] fdr < 0.05 were defined as statistically significant. bootstrap resampling was used to generate probability values as implemented in pvclust []., pathway analysis of mirnas was performed with diana-mirpath v3.0 software available from http://snf-515788.vm.okeanos.grnet.gr/ []. the diana-tarbase v7.0 was selected as the mirnatarget prediction algorithm []. for functional annotation, […]

2017
PMCID: 5685598
PMID: 29136041
DOI: 10.1371/journal.pone.0187973

[…] their relative abundance with a benjamini-hochberg corrected p-value (fdr) ≤ 0.05 were considered significant []., for the identification of the networks and pathways of the selected mirnas we used diana mirpath (v3.0) []. we evaluated mirna dysregulation in ln using mir2disease [], phenomir [] for information about mirnas exhibiting a differential regulation in disease and other biological […]

2016
PMCID: 4996855
PMID: 27475403
DOI: 10.1016/j.gpb.2016.04.005

[…] sets of mirnas between different tissues and platforms are generated using venny v2.0 (http://bioinfogp.cnnb.csic.es/tools/venny/index.html). mieaa (http://www.ccb.uni saarland.de/mieaa_tool) and diana mirpath v.2.0 were used for mirna target prediction and pathway analysis. all given lists of mirnas are translated and annotated according to mirbase v14 nomenclature., cs conducted […]

2016
PMCID: 5120312
PMID: 27876829
DOI: 10.1038/srep36904

[…] correlation coefficient more than 50%. the clusters can be seen in . representative mirnas for each cluster are shown. only the top three kegg pathways associated with the mirnas in each cluster by diana mirpath are shown. abbreviations: kegg, kyoto encyclopedia of genes and genomes; mapk, mitogen-activated protein kinase; pi3k, phosphatidylinositol-4, 5-bisphosphate 3-kinase; tgf, transforming […]


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DIANA-miRPath in publications

 (251)
PMCID: 5946432
PMID: 29747626
DOI: 10.1186/s12936-018-2330-5

[…] included in the expressionsuite analysis software. statistical calculations were performed using multiple t tests—one per row, with fewer assumptions., microarray results were analyzed with diana mirpath version 3 [] and ingenuity® pathway analysis—ipa (ingenuity® system, http://www.ingenuity.com) to combine filtering and mirna matching to mrna targets in order to provide insight […]

PMCID: 5933750
PMID: 29723239
DOI: 10.1371/journal.pone.0196666

[…] predicts biological targets of mirnas by searching for the presence of 8mer, 7mer, and 6mer sites that match the seed region of each mirna []. prediction of mirna functions were determined by using diana-mirpath v3. 0 (http://www.microrna.gr/mirpathv3) []. functional protein association networks were identified by using string 10.5 (https://string-db.org/) []. cellular kegg pathway enrichments […]

PMCID: 5930968
PMID: 29716593
DOI: 10.1186/s12943-018-0833-x

[…] were used in conjunction to predict circrna-mirna-target gene associations. first of all, mirna candidates were identified in kegg cancer-related pathways within the circrna-mirna network using the diana-mirpath v.3 platform, which has been reported in previous study [], the candidate circrna(s) were matched against the seed sequences of predicted target mirna candidate(s) using the intarna […]

PMCID: 5907383
PMID: 29669525
DOI: 10.1186/s12885-018-4364-z

[…] was performed for mirnas that were found to be up-regulated (p < 0.09) or only expressed by oscc patients. kyoto encyclopedia of gene and genomes (kegg) pathway analysis was performed through the diana-mirpath v.3.0 [] online software and mirna targets were searched on microt-cds []. results were merged by a “pathway-union” criterion. the p value was calculated by diana software online with: […]

PMCID: 5911478
PMID: 29713312
DOI: 10.3389/fendo.2018.00158

[…] hierarchical clustering and heatmaps were performed and created using morpheus from broad institute (https://software.broadinstitute.org/morpheus/).pathway enrichment analysis were executed using diana-mirpath v3.0 () and significance was determined using fisher’s exact test., for mrna sequencing, preprocessing of data were conducted on torrent server using torrent suite v4.4.2 software (life […]


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DIANA-miRPath institution(s)
DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, Volos, Greece; Laboratory for Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School of Athens, University of Athens, Athens, Greece; ‘Athena’ Research and Innovation Center, Athens, Greece; University of Peloponnisos, Department of Informatics and Telecommunications, Tripoli, Greece
DIANA-miRPath funding source(s)
‘TOM’ (4580), ‘ARISTEIA’ Action of the ‘OPERATIONAL PROGRAMME EDUCATION AND LIFELONG LEARNING’; European Social Fund (ESF) and National Resources; John S. Latsis Public Benefit Foundation; ‘MEDA’ (MIS 448842), Development Grants For Research Institutions – KRIPIS, General Secretariat for Research and Technology, Ministry of Education, Greece; European Regional Development Fund

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