MiRTargetLink—miRNAs, genes and interaction networks

International Journal of Molecular Sciences

Volumn 17, Issue 4, 2016, Pages

  Hamberg, Maarten ^a   Backes, Christina ^a   Fehlmann, Tobias ^a   Hart, Martin ^b   Meder, Benjamin ^c   Meese, Eckart ^b   Keller, Andreas ^a  

^a SAARLAND UNIVERSITY   (Germany)

^b SAARLAND UNIVERSITY   (Germany)

^c UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

Genes; Interaction networks; MiRNAs; MiRTargetkLink

Indexed keywords

MICRORNA; MICRORNA 107;

ARTICLE; CONGESTIVE CARDIOMYOPATHY; GENE IDENTIFICATION; GENE INTERACTION; GENE MAPPING; GENE TARGETING; GENETIC ANALYSIS; HEART RIGHT VENTRICLE DYSPLASIA; HIGH THROUGHPUT SCREENING; LUCIFERASE ASSAY; MICROARRAY ANALYSIS; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; HUMAN; INTERNET; SOFTWARE;

DATABASES, GENETIC; GENE REGULATORY NETWORKS; HUMANS; INTERNET; MICRORNAS; SOFTWARE;

EID: 84963752566     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms17040564     Document Type: Article

References (19)

1. Snel, B.; Lehmann, G.; Bork, P.; Huynen, M.A. String: A web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 2000, 28, 3442–3444. [CrossRef] [PubMed]
2. Szklarczyk, D.; Franceschini, A.; Wyder, S.; Forslund, K.; Heller, D.; Huerta-Cepas, J.; Simonovic, M.; Roth, A.; Santos, A.; Tsafou, K.P.; et al. String v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015, 43, D447–D452. [CrossRef] [PubMed]
3. Laczny, C.; Leidinger, P.; Haas, J.; Ludwig, N.; Backes, C.; Gerasch, A.; Kaufmann, M.; Vogel, B.; Katus, H.A.; Meder, B.; et al. miRTrail—A comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. BMC Bioinform. 2012, 13. [CrossRef] [PubMed]
4. Hamed, M.; Spaniol, C.; Nazarieh, M.; Helms, V. TFmiR: A web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks. Nucleic Acids Res. 2015, 43, W283–W288. [CrossRef] [PubMed]
5. Moreira, F.C.; Dustan, B.; Hamoy, I.G.; Ribeiro-Dos-Santos, A.M.; Dos Santos, A.R. TargetCompare: A web interface to compare simultaneous miRNAs targets. Bioinformation 2014, 10, 602–605. [CrossRef] [PubMed]
6. Smoot, M.E.; Ono, K.; Ruscheinski, J.; Wang, P.L.; Ideker, T. Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics 2011, 27, 431–432. [CrossRef] [PubMed]
7. Chou, C.H.; Chang, N.W.; Shrestha, S.; Hsu, S.D.; Lin, Y.L.; Lee, W.H.; Yang, C.D.; Hong, H.C.; Wei, T.Y.; Tu, S.J.; et al. miRTarBase 2016: Updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res. 2016, 44, D239–D247. [CrossRef] [PubMed]
8. Enright, A.J.; John, B.; Gaul, U.; Tuschl, T.; Sander, C.; Marks, D.S. MicroRNA targets in Drosophila. Genome Biol. 2003, 5. [CrossRef] [PubMed]
9. Backes, C.; Keller, A.; Kuentzer, J.; Kneissl, B.; Comtesse, N.; Elnakady, Y.A.; Muller, R.; Meese, E.; Lenhof, H.P. GeneTrail—Advanced gene set enrichment analysis. Nucleic Acids Res. 2007, 35, W186–W192. [CrossRef] [PubMed]
10. miRTargetLink. Available online: http://ccb-web.cs.uni-saarland.de/mirtargetlink (accessed on 8 April 2016).
11. VIS.js. Available online: http://www.visjs.org (accessed on 8 April 2016).
12. Kozomara, A.; Griffiths-Jones, S. miRBase: Annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014, 42, D68–D73. [CrossRef] [PubMed]
13. miEAA. Available online: www.ccb.uni-saarland.de/mieaa_tool/mirna_version_converter (accessed on 8 April 2016).
14. Duan, L.; Xiong, X.; Liu, Y.; Wang, J. miRNA-1: Functional roles and dysregulation in heart disease. Mol. Biosyst. 2014, 10, 2775–2782. [CrossRef] [PubMed]
15. Nabialek, E.; Wanha, W.; Kula, D.; Jadczyk, T.; Krajewska, M.; Kowalowka, A.; Dworowy, S.; Hrycek, E.; Wludarczyk, W.; Parma, Z.; et al. Circulating microRNAs (miR-423-5p, miR-208a and miR-1) in acute myocardial infarction and stable coronary heart disease. Minerva Cardioangiol. 2013, 61, 627–637. [PubMed]
16. Higashi, K.; Yamada, Y.; Minatoguchi, S.; Baba, S.; Iwasa, M.; Kanamori, H.; Kawasaki, M.; Nishigaki, K.; Takemura, G.; Kumazaki, M.; et al. MicroRNA-145 repairs infarcted myocardium by accelerating cardiomyocyte autophagy. Am. J. Physiol. Heart Circ. Physiol. 2015, 309, H1813–H1826. [CrossRef] [PubMed]
17. Liu, Q.; Du, G.Q.; Zhu, Z.T.; Zhang, C.; Sun, X.W.; Liu, J.J.; Li, X.; Wang, Y.S.; Du, W.J. Identification of apoptosis-related microRNAs and their target genes in myocardial infarction post-transplantation with skeletal myoblasts. J. Transl. Med. 2015, 13. [CrossRef] [PubMed]
18. Stockel, D.; Kehl, T.; Trampert, P.; Schneider, L.; Backes, C.; Ludwig, N.; Gerasch, A.; Kaufmann, M.; Gessler, M.; Graf, N.; et al. Multi-omics Enrichment Analysis using the GeneTrail2Web Service. Bioinformatics 2016, 32. [CrossRef] [PubMed]
19. Backes, C.; Meese, E.; Lenhof, H.P.; Keller, A. A dictionary on microRNAs and their putative target pathways. Nucleic Acids Res. 2010, 38, 4476–4486. [CrossRef] [PubMed]