MiRPathDB: A new dictionary on microRNAs and target pathways

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D90-D96

  Backes, Christina ^a   Kehl, Tim ^a   Stöckel, Daniel ^a   Fehlmann, Tobias ^a   Schneider, Lara ^a   Meese, Eckart ^b   Lenhof, Hans Peter ^a   Keller, Andreas ^a  

^a SAARLAND UNIVERSITY   (Germany)

^b SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; COMPUTER ANALYSIS; GENE CLUSTER; GENE LOCATION; GENE TARGETING; GENETIC ANALYSIS; GENETIC DATABASE; HUMAN; INFORMATION PROCESSING; MICRORNA PATHWAY DICTIONARY DATABASE; MUS MUSCULUS; NONHUMAN; REGULATORY MECHANISM; VALIDATION STUDY; ANIMAL; GENE EXPRESSION REGULATION; METABOLISM; MOUSE; NUCLEIC ACID DATABASE;

MICRORNA;

ANIMALS; DATABASES, NUCLEIC ACID; GENE EXPRESSION REGULATION; HUMANS; MICE; MICRORNAS;

EID: 85014201942     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw926     Document Type: Article

References (28)

1. Ambros, V. (2001) microRNAs: Tiny regulators with great potential. Cell, 107, 823-826.
2. Griffiths-Jones, S. (2004) The microRNA Registry. Nucleic Acids Res., 32, D109-D111.
3. Griffiths-Jones, S., Saini, H.K., van Dongen, S. and Enright, A.J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36, D154-D158.
4. Akhtar, M.M., Micolucci, L., Islam, M.S., Olivieri, F. and Procopio, A.D. (2016) Bioinformatic tools for microRNA dissection. Nucleic Acids Res., 44, 24-44.
5. Chiromatzo, A.O., Oliveira, T.Y., Pereira, G., Costa, A.Y., Montesco, C.A., Gras, D.E., Yosetake, F., Vilar, J.B., Cervato, M., Prado, P.R. et al. (2007) miRNApath: A database of miRNAs, target genes and metabolic pathways. Genet. Mol. Res., 6, 859-865.
6. Kowarsch, A., Preusse, M., Marr, C. and Theis, F.J. (2011) miTALOS: Analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. RNA, 17, 809-819.
7. Vlachos, I.S., Kostoulas, N., Vergoulis, T., Georgakilas, G., Reczko, M., Maragkakis, M., Paraskevopoulou, M.D., Prionidis, K., Dalamagas, T. and Hatzigeorgiou, A.G. (2012) DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res., 40, W498-W504.
8. Vlachos, I.S., Zagganas, K., Paraskevopoulou, M.D., Georgakilas, G., Karagkouni, D., Vergoulis, T., Dalamagas, T. and Hatzigeorgiou, A.G. (2015) DIANA-miRPath v3.0: Deciphering microRNA function with experimental support. Nucleic Acids Res., 43, W460-W466.
9. Stockel, D., Kehl, T., Trampert, P., Schneider, L., Backes, C., Ludwig, N., Gerasch, A., Kaufmann, M., Gessler, M., Graf, N. et al. (2016) Multi-omics enrichment analysis using the GeneTrail2 web service. Bioinformatics, 32, 1502-1508.
10. Capece, V., Garcia Vizcaino, J.C., Vidal, R., Rahman, R.U., Pena Centeno, T., Shomroni, O., Suberviola, I., Fischer, A. and Bonn, S. (2015) Oasis: online analysis of small RNA deep sequencing data. Bioinformatics, 31, 2205-2207.
11. Backes, C., Meese, E., Lenhof, H.P. and Keller, A. (2010) A dictionary on microRNAs and their putative target pathways. Nucleic Acids Res., 38, 4476-4486.
12. Kozomara, A. and Griffiths-Jones, S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res., 42, D68-D73.
13. Backes, C., Keller, A., Kuentzer, J., Kneissl, B., Comtesse, N., Elnakady, Y.A., Muller, R., Meese, E. and Lenhof, H.P. (2007) GeneTrail-advanced gene set enrichment analysis. Nucleic Acids Res., 35, W186-W192.
14. Das, N. (2012) MicroRNA Targets-How to predict? Bioinformation, 8, 841-845.
15. Vlachos, I.S., Paraskevopoulou, M.D., Karagkouni, D., Georgakilas, G., Vergoulis, T., Kanellos, I., Anastasopoulos, I.L., Maniou, S., Karathanou, K., Kalfakakou, D. et al. (2015) DIANA-TarBase v7.0: Indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res., 43, D153-D159.
16. 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. (2016) miRTarBase 2016: Updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res., 44, D239-D247.
17. Kanehisa, M. and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
18. Stein, L.D. (2004) Using the Reactome database. Curr. Protoc. Bioinformatics, doi:10.1002/0471250953.bi0807s7.
19. Nishimura, D. (2004) BioCarta. Biotech Software Internet Report, 2, 117-120.
20. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
21. Schaefer, C.F., Anthony, K., Krupa, S., Buchoff, J., Day, M., Hannay, T. and Buetow, K.H. (2009) PID: the Pathway Interaction Database. Nucleic Acids Res., 37, D674-D679.
22. Jewison, T., Su, Y., Disfany, F.M., Liang, Y., Knox, C., Maciejewski, A., Poelzer, J., Huynh, J., Zhou, Y., Arndt, D. et al. (2014) SMPDB 2.0: big improvements to the Small Molecule Pathway Database. Nucleic Acids Res., 42, D478-D484.
23. Bleazard, T., Lamb, J.A. and Griffiths-Jones, S. (2015) Bias in microRNA functional enrichment analysis. Bioinformatics, 31, 1592-1598.
24. Paraskevopoulou, M. D., Georgakilas, G., Kostoulas, N., Vlachos, I. S., Vergoulis, T., Reczko, M., Filippidis, C., Dalamagas, T. and Hatzigeorgiou, A.G. (2013). DIANA-microT web server v5. 0: service integration into miRNA functional analysis workflows. Nucleic Acids Res., 41, W169-W173.
25. Wong, N. and Wang, X. (2014). miRDB: An online resource for microRNA target prediction and functional annotations. Nucleic Acids Res., 43, D146-D152.
26. Agarwal, V., Bell, G. W., Nam, J. W. and Bartel, D. P. (2015). Predicting effective microRNA target sites in mammalian mRNAs. Elife, 4, e05005.
27. Tange, O. (2011) GNU Parallel-The Command-Line Power Tool. login: The USENIX Magazine, 2011, 42-47.
28. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L. et al. (2004). The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.