RNAcentral: A vision for an international database of RNA sequences

RNA

Volumn 17, Issue 11, 2011, Pages 1941-1946

  Bateman, Alex ^a   Agrawal, Shipra ^b,c   Birney, Ewan ^a   Bruford, Elspeth A ^a   Bujnicki, Janusz M ^d,e   Cochrane, Guy ^a   Cole, James R ^f   Dinger, Marcel E ^g   Enright, Anton J ^a   Gardner, Paul P ^a   Gautheret, Daniel ^h   Griffiths Jones, Sam ⁱ   Harrow, Jen ^a   Herrero, Javier ^a   Holmes, Ian H ^j   Huang, Hsien D A ^k   Kelly, Krystyna A ^l   Kersey, Paul ^a   Kozomara, A N A ⁱ   Lowe, Todd M ^m   Marz, Manja ⁿ   Moxon, Simon ^o   Pruitt, Kim D ^p   Samuelsson, Tore ^q   Stadler, Peter F ^r   Vilella, Albert J ^a   Vogel, Jan Hinnerk ^a   Williams, Kelly P ^s   Wright, Mathew W ^a   Zwieb, Christian ^t   more..

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b Institute of Bioinformatics and Applied Biotechnology (IBAB)   (India)

^c BioCOS Life Sciences Private Limited   (India)

^d INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^e INSTITUTE OF MOLECULAR PHYSICS   (Poland)

^f MICHIGAN STATE UNIVERSITY   (United States)

^g UNIVERSITY OF QUEENSLAND   (Australia)

^h CNRS   (France)

ⁱ UNIVERSITY OF MANCHESTER   (United Kingdom)

^j University of California   (United States)

^k NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^l UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^m University of California Santa Cruz   (United States)

ⁿ PHILIPPS UNIVERSITY MARBURG   (Germany)

^o UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^p NATIONAL INSTITUTES OF HEALTH   (United States)

^q UNIVERSITY OF GOTHENBURG   (Sweden)

^r UNIVERSITY OF LEIPZIG   (Germany)

^s SANDIA NATIONAL LABORATORIES   (United States)

^t University of Texas Health Science Center   (United States)

more..

Author keywords

Federation; Noncoding RNA; Sequence database

Indexed keywords

MICRORNA; SMALL INTERFERING RNA;

ARTICLE; BIOTECHNOLOGY; FOOD SECURITY; GENETIC RESOURCE; MEDICAL RESEARCH; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; RNACENTRAL; SEQUENCE DATABASE;

ANIMALS; BASE SEQUENCE; DATABASES, NUCLEIC ACID; HUMANS; RNA;

ANIMALIA;

EID: 80054748784     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2750811     Document Type: Article

References (50)

1. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. 2011. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 39: D146-D151.
2. Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C. 2006. The tmRDB and SRPDB resources. Nucleic Acids Res 34: D163-D168.
3. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. 2005. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123: 1279-1291. (Pubitemid 41821785)
4. Braconi C, Valeri N, Kogure T, Gasparini P, Huang N, Nuovo GJ, Terracciano L, Croce CM, Patel T. 2011. Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma. Proc Natl Acad Sci 108: 786-791.
5. Buiting K. 2010. Prader-Willi syndrome and Angelman syndrome. Am J Med Genet C Semin Med Genet 154C: 366-376.
6. Chan PP, Lowe TM. 2009. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37: D93-D97.
7. Christov CP, Trivier E, Krude T. 2008. Noncoding human Y RNAs are overexpressed in tumours and required for cell proliferation. Br J Cancer 98: 981-988. (Pubitemid 351341611)
8. Citti L, Rainaldi G. 2005. Synthetic hammerhead ribozymes as therapeutic tools to control disease genes. Curr Gene Ther 5: 11-24. (Pubitemid 40246739)
9. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
10. Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Grosjean H, Rother K. 2009. MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res 37: D118-D121.
11. Elmen J, Lindow M, Schutz S, Lawrence M, Petri A, Obad S, Lindholm M, Hedtjarn M, Hansen HF, Berger U, et al. 2008. LNA-mediated microRNA silencing in non-human primates. Nature 452: 896-899. (Pubitemid 351550859)
12. Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, et al. 2011. Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res 39: D141-D145.
13. Grissa I, Vergnaud G, Pourcel C. 2007. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8: 172. doi: 10.1186/1471-2105-8-172.
14. Gueneau de Novoa P, Williams KP. 2004. The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts. Nucleic Acids Res 32: D104-D108. (Pubitemid 38081614)
15. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
16. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, et al. 2005. A microRNA polycistron as a potential human oncogene. Nature 435: 828-833. (Pubitemid 40839734)
17. Huang HY, Chang HY, Chou CH, Tseng CP, Ho SY, Yang CD, Ju YW, Huang HD. 2009. sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res 37: D150-D154.
18. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al. 2009. InterPro: the integrative protein signature database. Nucleic Acids Res 37: D211-D215.
19. Johansson J, Mandin P, Renzoni A, Chiaruttini C, Springer M, Cossart P. 2002. An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 110: 551-561. (Pubitemid 35247836)
20. Jopling CL, Yi M, Lancaster AM, Lemon SM, Sarnow P. 2005. Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science 309: 1577-1581. (Pubitemid 41266486)
21. Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S, Gingeras TR. 2005. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res 15: 987-997. (Pubitemid 40994219)
22. Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kahari A, et al. 2010. Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res 38: D563-D569.
23. Kozomara A, Griffiths-Jones S. 2011. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-D157.
24. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294: 853-858. (Pubitemid 33032103)
25. Lai EC. 2003. RNA sensors and riboswitches: self-regulating messages. Curr Biol 13: R285-R291. (Pubitemid 36391929)
26. Lau NC, Lim LP, Weinstein EG, Bartel DP. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862. (Pubitemid 33032104)
27. Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP, Kingston RE. 2006. Characterization of the piRNA complex from rat testes. Science 313: 363-367. (Pubitemid 44480963)
28. Lee RC, Ambros V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864. (Pubitemid 33032105)
29. Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tarraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, et al. 2011. The European Nucleotide Archive. Nucleic Acids Res 39: D28-D31.
30. Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, et al. 2009. An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. Nat Genet 41: 614-618.
31. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, et al. 2005. MicroRNA expression profiles classify human cancers. Nature 435: 834-838. (Pubitemid 40839735)
32. Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engstrom PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, et al. 2006. Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet 2: e62. doi: 10.1371/journal.pgen.0020062.
33. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, et al. 2009. Finding the missing heritability of complex diseases. Nature 461: 747-753.
34. Mlotshwa S, Pruss GJ, Vance V. 2008. Small RNAs in viral infection and host defense. Trends Plant Sci 13: 375-382.
35. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. (Pubitemid 351911867)
36. Pang KC, Stephen S, Dinger ME, Engstrom PG, Lenhard B, Mattick JS. 2007. RNAdb 2.0-an expanded database of mammalian non-coding RNAs. Nucleic Acids Res 35: D178-D182. (Pubitemid 46056194)
37. Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. 2004. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 18: 2368-2379. (Pubitemid 39304684)
38. Perez de Nanclares G, Castano L, Martul P, Rica I, Vela A, Sanjurjo P, Aldamiz-Echevarria K, Martinez R, Sarrionandia MJ. 2001. Molecular analysis of hereditary hyperferritinemia-cataract syndrome in a large Basque family. J Pediatr Endocrinol Metab 14: 295-300. (Pubitemid 32229762)
39. Pruitt KD, Tatusova T, Klimke W, Maglott DR. 2009. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 37: D32-D36.
40. Ridanpää M, van Eenennaam H, Pelin K, Chadwick R, Johnson C, Yuan B, vanVenrooij W, Pruijn G, Salmela R, Rockas S, et al. 2001. Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, cartilage-hair hypoplasia. Cell 104: 195-203. (Pubitemid 32174836)
41. Rodnina MV, Beringer M, Wintermeyer W. 2007. How ribosomes make peptide bonds. Trends Biochem Sci 32: 20-26. (Pubitemid 46038738)
42. Sai Lakshmi S, Agrawal S. 2008. piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Nucleic Acids Res 36: D173-D177.
43. Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA. 2011. genenames.org: the HGNC resources in 2011. Nucleic Acids Res 39: D514-D519.
44. Sunkar R, Kapoor A, Zhu JK. 2006. Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 18: 2051-2065. (Pubitemid 44260196)
45. Tenson T, Mankin A. 2006. Antibiotics and the ribosome. Mol Microbiol 59: 1664-1677.
46. Trindade I, Capitao C, Dalmay T, Fevereiro MP, Santos DM. 2010. miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 231: 705-716.
47. Tsagris EM, Martinez de Alba AE, Gozmanova M, Kalantidis K. 2008. Viroids. Cell Microbiol 10: 2168-2179.
48. Valadkhan S, Mohammadi A, Jaladat Y, Geisler S. 2009. Protein-free small nuclear RNAs catalyze a two-step splicing reaction. Proc Natl Acad Sci 106: 11901-11906.
49. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert JL, Bartel DP, Crete P. 2004. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16: 69-79. (Pubitemid 39330153)
50. Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL. 2008. The vertebrate genome annotation (Vega) database. Nucleic Acids Res 36: D753-D760. (Pubitemid 351149819)