MiRCarta: A central repository for collecting miRNA candidates

Nucleic Acids Research

Volumn 46, Issue D1, 2018, Pages D160-D167

  Backes, Christina ^a   Fehlmann, Tobias ^a   Kern, Fabian ^a   Kehl, Tim ^a   Lenhof, Hans Peter ^a   Meese, Eckart ^a   Keller, Andreas ^a  

^a SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA PRECURSOR;

3' UNTRANSLATED REGION; ALGORITHM; ARTICLE; CONTROLLED STUDY; DISEASE ASSOCIATION; HUMAN; HUMAN TISSUE; NEXT GENERATION SEQUENCING; NUCLEIC ACID DATABASE; PREDICTION; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; TISSUE DISTRIBUTION; VALIDATION STUDY; ANIMAL; CHEMISTRY; CONFORMATION; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; SEQUENCE ANALYSIS;

ANIMALS; DATABASES, NUCLEIC ACID; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; NUCLEIC ACID CONFORMATION; RNA PRECURSORS; SEQUENCE ANALYSIS, RNA;

EID: 85040905802     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx851     Document Type: Article

References (40)

1. Bartel,D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
2. Sontheimer,E.J. and Carthew,R.W. (2005) Silence from within: endogenous siRNAs and miRNAs. Cell, 122, 9-12.
3. Filipowicz,W., Jaskiewicz,L., Kolb,F.A. and Pillai,R.S. (2005) Post-transcriptional gene silencing by siRNAs and miRNAs. Curr. Opin. Struct. Biol., 15, 331-341.
4. Li,Y.J., Ping,C., Tang,J. and Zhang,W. (2016) MicroRNA-455 suppresses non-small cell lung cancer through targeting ZEB1. Cell Biol. Int., 40, 621-628.
5. Keller,A., Leidinger,P., Steinmeyer,F., Stahler,C., Franke,A., Hemmrich-Stanisak,G., Kappel,A., Wright,I., Dorr,J., Paul,F. et al. (2014) Comprehensive analysis of microRNA profiles in multiple sclerosis including next-generation sequencing. Mult. Scler., 20, 295-303.
6. Keller,A., Leidinger,P., Vogel,B., Backes,C., ElSharawy,A., Galata,V., Muller,S., Marquart,S., Schrauder,M., Strick,R. et al. (2014) miRNAs can be generally associated with human pathologies as exemplified for miR-144. BMC Med., 12, 224.
7. Fenoglio,C., Ridolfi,E., Cantoni,C., De Riz,M., Bonsi,R., Serpente,M., Villa,C., Pietroboni,A.M., Naismith,R.T., Alvarez,E. et al. (2013) Decreased circulating miRNA levels in patients with primary progressive multiple sclerosis. Mult. Scler., 19, 1938-1942.
8. Keller,A., Leidinger,P., Bauer,A., Elsharawy,A., Haas,J., Backes,C., Wendschlag,A., Giese,N., Tjaden,C., Ott,K. et al. (2011) Toward the blood-borne miRNome of human diseases. Nat. Methods, 8, 841-843.
9. Roth,P., Keller,A., Hoheisel,J.D., Codo,P., Bauer,A.S., Backes,C., Leidinger,P., Meese,E., Thiel,E., Korfel,A. et al. (2015) Differentially regulated miRNAs as prognostic biomarkers in the blood of primary CNS lymphoma patients. Eur. J. Cancer, 51, 382-390.
10. Ma,J., Lin,Y., Zhan,M., Mann,D.L., Stass,S.A. and Jiang,F. (2015) Differential miRNA expressions in peripheral blood mononuclear cells for diagnosis of lung cancer. Lab. Invest., 95, 1197-1206.
11. Sayed,A.S., Xia,K., Yang,T.L. and Peng,J. (2013) Circulating microRNAs: a potential role in diagnosis and prognosis of acute myocardial infarction. Dis. Markers, 35, 561-566.
12. Keller,A., Backes,C., Haas,J., Leidinger,P., Maetzler,W., Deuschle,C., Berg,D., Ruschil,C., Galata,V., Ruprecht,K. et al. (2016) Validating Alzheimer's disease micro RNAs using next-generation sequencing. Alzheimers Dement., 12, 565-576.
13. Margue,C., Reinsbach,S., Philippidou,D., Beaume,N., Walters,C., Schneider,J.G., Nashan,D., Behrmann,I. and Kreis,S. (2015) Comparison of a healthy miRNome with melanoma patient miRNomes: are microRNAs suitable serum biomarkers for cancer? Oncotarget, 6, 12110-12127.
14. Kozomara,A. and Griffiths-Jones,S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res., 42, D68-D73.
15. Londin,E., Loher,P., Telonis,A.G., Quann,K., Clark,P., Jing,Y., Hatzimichael,E., Kirino,Y., Honda,S., Lally,M. et al. (2015) Analysis of 13 cell types reveals evidence for the expression of numerous novel primate-and tissue-specific microRNAs. Proc. Natl. Acad. Sci. U.S.A., 112, E1106-E1115.
16. Backes,C., Meder,B., Hart,M., Ludwig,N., Leidinger,P., Vogel,B., Galata,V., Roth,P., Menegatti,J., Grasser,F. et al. (2016) Prioritizing and selecting likely novel miRNAs from NGS data. Nucleic Acids Res., 44, e53.
17. Friedlander,M.R., Mackowiak,S.D., Li,N., Chen,W. and Rajewsky,N. (2011) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res., 40, 37-52.
18. Jha,A., Panzade,G., Pandey,R. and Shankar,R. (2015) A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm. Nucleic Acids Res., 43, 8713-8724.
19. Vitsios,D.M., Davis,M.P., van Dongen,S. and Enright,A.J. (2016) Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis. Nucleic Acids Res., 45, 1079-1090.
20. Fromm,B., Billipp,T., Peck,L.E., Johansen,M., Tarver,J.E., King,B.L., Newcomb,J.M., Sempere,L.F., Flatmark,K., Hovig,E. et al. (2015) A uniform system for the annotation of vertebrate microRNA genes and the evolution of the human microRNAome. Annu. Rev. Genet., 49, 213-242.
21. Ludwig,N., Becker,M., Schumann,T., Speer,T., Fehlmann,T., Keller,A. and Meese,E. (2017) Bias in recent miRBase annotations potentially associated with RNA quality issues. Sci. Rep., 7, 5162.
22. Fehlmann,T., Backes,C., Kahraman,M., Haas,J., Ludwig,N., Posch,A., W urstle,M., Hubenthal,M., Franke,A., Meder,B. et al. (2017) Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs. Nucleic Acids Res., 45, 8731-8744.
23. Kodama,Y., Shumway,M., Leinonen,R. and International Nucleotide Sequence Database, C. (2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res., 40, D54-D56.
24. Cancer Genome Atlas Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061-1068.
25. 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.
26. Agarwal,V., Bell,G.W., Nam,J.W. and Bartel,D.P. (2015) Predicting effective microRNA target sites in mammalian mRNAs. Elife, 4, doi:10.7554/eLife.05005.
27. 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.
28. Li,Y., Qiu,C., Tu,J., Geng,B., Yang,J., Jiang,T. and Cui,Q. (2014) HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res., 42, D1070-D1074.
29. Backes,C., Kehl,T., Stockel,D., Fehlmann,T., Schneider,L., Meese,E., Lenhof,H.P. and Keller,A. (2017) miRPathDB: a new dictionary on microRNAs and target pathways. Nucleic Acids Res., 45, D90-D96.
30. Hamberg,M., Backes,C., Fehlmann,T., Hart,M., Meder,B., Meese,E. and Keller,A. (2016) MiRTargetLink-miRNAs, genes and interaction networks. Int. J. Mol. Sci., 17, 564.
31. Ludwig,N., Leidinger,P., Becker,K., Backes,C., Fehlmann,T., Pallasch,C., Rheinheimer,S.,Meder,B., Stahler,C., Meese,E. et al. (2016) Distribution of miRNA expression across human tissues. Nucleic Acids Res., 44, 3865-3877.
32. Jiang,Q., Wang,Y., Hao,Y., Juan,L., Teng,M., Zhang,X., Li,M., Wang,G. and Liu,Y. (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res., 37, D98-D104.
33. 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.
34. Coordinators,N.R. (2015) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 43, D6-D17.
35. Langmead,B., Trapnell,C., Pop,M. and Salzberg,S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
36. Kerpedjiev,P., Hammer,S. and Hofacker,I.L. (2015) Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinformatics, 31, 3377-3379.
37. Lorenz,R., Bernhart,S.H., Honer Zu Siederdissen,C., Tafer,H., Flamm,C., Stadler,P.F. and Hofacker,I.L. (2011) ViennaRNA Package 2.0. Algorithms Mol. Biol., 6, 26.
38. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
39. Van Peer,G., Lefever,S., Anckaert,J., Beckers,A., Rihani,A., Van Goethem,A., Volders,P.J., Zeka,F., Ongenaert,M., Mestdagh,P. et al. (2014) miRBase Tracker: keeping track of microRNA annotation changes. Database (Oxford), 2014, bau080.
40. Friedlander,M.R., Lizano,E., Houben,A.J., Bezdan,D., Banez-Coronel,M., Kudla,G., Mateu-Huertas,E., Kagerbauer,B., Gonzalez,J., Chen,K.C. et al. (2014) Evidence for the biogenesis of more than 1,000 novel human microRNAs. Genome Biol., 15, R57