MiRBase: Annotating high confidence microRNAs using deep sequencing data

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Kozomara, Ana ^a   Griffiths Jones, Sam ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; DICER;

APPLICATION SERVICE PROVIDER; ARTICLE; CLIENT SERVER APPLICATION; CLINICAL DATA REPOSITORY; DATA BASE; HUMAN; INFORMATION SYSTEM; MIRBASE; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; DROSOPHILA MELANOGASTER; GENE LOCUS; GENE MAPPING; MIRBASE DATABASE; NUCLEIC ACID DATABASE; PEPTIDE MAPPING; PLANT GENOME; RNA STRUCTURE; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; ANIMAL; CHEMISTRY; HIGH THROUGHPUT SEQUENCING; INTERNET; MOLECULAR GENETICS; MOUSE; SEQUENCE ANALYSIS;

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

EID: 84891818318     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1181     Document Type: Article

References (26)

1. Okamura, K., Phillips, M.D., Tyler, D.M., Duan, H., Chou, Y. and Lai, E.C. (2008) The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nat. Struct. Mol. Biol., 15, 354-363.
2. Yang, J.-S., Phillips, M.D., Betel, D., Mu, P., Ventura, A., Siepel, A.C., Chen, K.C. and Lai, E.C. (2011) Widespread regulatory activity of vertebrate microRNA* species. RNA, 17, 312-326.
3. Marco, A., Hui, J.H.L., Ronshaugen, M. and Griffiths-Jones, S. (2010) Functional shifts in insect microRNA evolution. Genome Biol. Evol., 2, 686-696.
4. Griffiths-Jones, S., Hui, J.H.L., Marco, A. and Ronshaugen, M. (2011) MicroRNA evolution by arm switching. EMBO Rep., 12, 172-177.
5. Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
6. 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.
7. Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A. and Enright, A.J. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 34, D140-D144.
8. Griffiths-Jones, S. (2004) The microRNA Registry. Nucleic Acids Res., 32, D109-D111.
9. Meng, Y., Shao, C., Wang, H. and Chen, M. (2012) Are all the miRBase-registered microRNAs true? A structure-and expression-based re-examination in plants. RNA Biol., 9, 249-253.
10. Wang, X. and Liu, X.S. (2011) Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. Elegans and Drosophila. Front. Genet., 2, 25.
11. Hansen, T.B., Kjems, J. and Bramsen, J.B. (2011) Enhancing miRNA annotation confidence in miRBase by continuous cross dataset analysis. RNA Biol., 8, 378-383.
12. Brown, M., Suryawanshi, H., Hafner, M., Farazi, T.A. and Tuschl, T. (2013) Mammalian miRNA curation through next-generation sequencing. Front. Genet., 4, 145.
13. Berezikov, E., Liu, N., Flynt, A.S., Hodges, E., Rooks, M., Hannon, G.J. and Lai, E.C. (2010) Evolutionary flux of canonical microRNAs and mirtrons in Drosophila. Nat. Genet., 42, 6-9.
14. Friedlander, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S. and Rajewsky, N. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415.
15. Barrett, T., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Holko, M. et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
16. Kodama, Y., Shumway, M., Leinonen, R. and International Nucleotide Sequence Database Collaboration. (2012) The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res., 40, D54-D56.
17. Harris, T.A., Yamakuchi, M., Ferlito, M., Mendell, J.T. and Lowenstein, C.J. (2008) MicroRNA-126 regulates endothelial expression of vascular cell adhesion molecule 1. Proc. Natl Acad. Sci. USA, 105, 1516-1521.
18. Cheloufi, S., Dos Santos, C.O., Chong, M.M. and Hannon, G.J. (2010) A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature, 465, 584-589.
19. Ruby, J.G., Jan, C.H. and Bartel, D.P. (2007) Intronic microRNA precursors that bypass Drosha processing. Nature, 448, 83-86.
20. Okamura, K., Hagen, J.W., Duan, H., Tyler, D.M. and Lai, E.C. (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell, 130, 89-100.
21. Berezikov, E., Chung, W.J., Willis, J., Cuppen, E. and Lai, E.C. (2007) Mammalian mirtron genes. Mol. Cell, 28, 328-336.
22. Good, B.M., Clarke, E.L., de Alfaro, L. and Su, A.I. (2012) The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Res., 40, D1255-D1261.
23. Wang, J., Zhuang, J., Iyer, S., Lin, X.Y., Greven, M.C., Kim, B.H., Moore, J., Pierce, B.G., Dong, X., Virgil, D. et al. (2013) Factorbook.org: a Wiki-based database for transcription factorbinding data generated by the ENCODE consortium. Nucleic Acids Res., 41, D171-D176.
24. Daub, J., Gardner, P.P., Tate, J., Ramskold, D., Manske, M., Scott, W.G., Weinberg, Z., Griffiths-Jones, S. and Bateman, A. (2008) The RNA WikiProject: community annotation of RNA families. RNA, 14, 2462-2464.
25. Stehr, H., Duarte, J.M., Lappe, M., Bhak, J. and Bolser, D.M. (2010) PDBWiki: added value through community annotation of the Protein Data Bank. Database, baq009.
26. Kelder, T., van Iersel, M.P., Hanspers, K., Kutmon, M., Conklin, B.R., Evelo, C.T. and Pico, A.R. (2012) WikiPathways: building research communities on biological pathways. Nucleic Acids Res., 40, D1301-D1307.