DIANA-miRPath v4.0: expanding target-based miRNA functional analysis in cell-type and tissue contexts

Abstract DIANA-miRPath is an online miRNA analysis platform harnessing predicted or experimentally supported miRNA interactions towards the exploration of combined miRNA effects. In its latest version (v4.0, http://www.microrna.gr/miRPathv4), DIANA-miRPath breaks new ground by introducing the capaci...

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Bibliographic Details
Published in:Nucleic acids research 2023-07, Vol.51 (W1), p.W154-W159
Main Authors: Tastsoglou, Spyros, Skoufos, Giorgos, Miliotis, Marios, Karagkouni, Dimitra, Koutsoukos, Ioannis, Karavangeli, Anna, Kardaras, Filippos S, Hatzigeorgiou, Artemis G
Format: Article
Language:English
Subjects:
Cell Communication
Databases, Chemical
MicroRNAs - genetics
MicroRNAs - metabolism
Software
Web Server Issue
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Summary:Abstract DIANA-miRPath is an online miRNA analysis platform harnessing predicted or experimentally supported miRNA interactions towards the exploration of combined miRNA effects. In its latest version (v4.0, http://www.microrna.gr/miRPathv4), DIANA-miRPath breaks new ground by introducing the capacity to tailor its target-based miRNA functional analysis engine to specific biological and/or experimental contexts. Via a redesigned modular interface with rich interaction, annotation and parameterization options, users can now perform enrichment analysis on Gene Ontology (GO) terms, KEGG and REACTOME pathways, sets from Molecular Signatures Database (MSigDB) and PFAM. Included miRNA interaction sets are derived from state-of-the-art resources of experimentally supported (DIANA-TarBase v8.0, miRTarBase and microCLIP cell-type-specific interactions) or from in silico miRNA–target interactions (updated DIANA-microT-CDS and TargetScan predictions). Bulk and single-cell expression datasets from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx) and adult/fetal single-cell atlases are integrated and can be used to assess the expression of enriched term components across a wide range of states. A discrete module enabling enrichment analyses using CRISPR knock-out screen datasets enables the detection of selected miRNAs with potentially crucial roles within conditions under study. Notably, the option to upload custom interaction, term, expression and screen sets further expands the versatility of miRPath webserver. Graphical Abstract Graphical Abstract
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkad431