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Preusse, M. ; Theis, F.J. ; Müller, N.S.

miTALOS v2: Analyzing tissue specific microRNA function.

PLoS ONE 11:e0151771 (2016)
Verlagsversion DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
MicroRNAs are involved in almost all biological processes and have emerged as regulators of signaling pathways. We show that miRNA target genes and pathway genes are not uniformly expressed across human tissues. To capture tissue specific effects, we developed a novel methodology for tissue specific pathway analysis of miRNAs. We incorporated the most recent and highest quality miRNA targeting data (TargetScan and StarBase), RNA-seq based gene expression data (EBI Expression Atlas) and multiple new pathway data sources to increase the biological relevance of the predicted miRNA-pathway associations. We identified new potential roles of miR-199a-3p, miR-199b-3p and the miR-200 family in hepatocellular carcinoma, involving the regulation of metastasis through MAPK and Wnt signaling. Also, an association of miR-571 and Notch signaling in liver fibrosis was proposed. To facilitate data update and future extensions of our tool, we developed a flexible database backend using the graph database neo4j. The new backend as well as the novel methodology were included in the updated miTALOS v2, a tool that provides insights into tissue specific miRNA regulation of biological pathways. miTALOS v2 is available at http://mips.helmholtz-muenchen.de/mitalos.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter Epithelial-mesenchymal Transition; Transcriptome-wide Identification; Rna-binding Protein; Hepatocellular-carcinoma; Target Sites; Cancer Cells; Expression; Liver; Gene; Proliferation
Sprache englisch
Veröffentlichungsjahr 2016
HGF-Berichtsjahr 2016
ISSN (print) / ISBN 1932-6203
Zeitschrift PLoS ONE
Quellenangaben Band: 11, Heft: 3, Seiten: , Artikelnummer: e0151771 Supplement: ,
Verlag Public Library of Science (PLoS)
Verlagsort Lawrence, Kan.
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)
Institute of Diabetes and Regeneration Research (IDR)
POF Topic(s) 30205 - Bioengineering and Digital Health
30201 - Metabolic Health
Forschungsfeld(er) Enabling and Novel Technologies
Helmholtz Diabetes Center
PSP-Element(e) G-503800-001
G-502300-001
PubMed ID 26998997
DOI 10.1371/journal.pone.0151771
WOS ID WOS:000372694700063
Scopus ID 84962124791
Erfassungsdatum 2016-03-23
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