CSRDB: A small RNA integrated database and browser resource for cereals

Nucleic Acids Research

Volumn 35, Issue SUPPL. 1, 2007, Pages

  Johnson, Cameron ^a   Bowman, Lewis ^a   Adai, Alex T ^c   Vance, Vicki ^b   Sundaresan, Venkatesan ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF SOUTH CAROLINA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PLANT RNA; SMALL INTERFERING RNA;

ARTICLE; BIOINFORMATICS; CEREAL; CEREAL SMALL RNA DATABASE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE MAPPING; HIGH THROUGHPUT SCREENING; INFORMATION RETRIEVAL; INFORMATION STORAGE; INTERNET; MAIZE; NONHUMAN; NUCLEIC ACID DATABASE; PLANT GENETICS; PRIORITY JOURNAL; RICE; RNA SEQUENCE; WEB BROWSER;

DATABASES, NUCLEIC ACID; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; GENOMICS; INTERNET; MICRORNAS; ORYZA SATIVA; RNA, MESSENGER; RNA, SMALL INTERFERING; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE; ZEA MAYS;

ZEA MAYS;

EID: 33846120020     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl991     Document Type: Article

References (17)

1. Meins,F., Jr, Si-Ammour,A. and Blevins,T. (2005) RNA silencing systems and their relevance to plant development. Annu. Rev. Cell Dev. Biol., 21, 297-318.
2. Willmann,M.R. and Poethig,R.S. (2005) Time to grow up: The temporal role of small RNAs in plants. Curr. Opin. Plant Biol., 8, 548-552.
3. Mallory,A.C. and Vaucheret,H. (2006) Functions of microRNAs and related small RNAs in plants. Nature Genet., 38, S31-S36.
4. Jones-Rhoades,M.W., Bartel,D.P. and Bartel,B. (2006) MicroRNAS and Their Regulatory Roles in Plants. Annu. Rev. Plant Biol., 57, 19-53.
5. Margulies,M., Egholm,M., Altman,W.E., Attiya,S., Bader,J.S., Bemben,L.A., Berka,J., Braverman,M.S., Chen,Y.J., Chen,Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
6. Lau,N.C., Lim,L.P., Weinstein,E.G. and Bartel,D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858-862.
7. Yuan,Q., Ouyang,S., Wang,A., Zhu,W., Maiti,R., Lin,H., Hamilton,J., Haas,B., Sultana,R., Cheung,F. et al. (2005) The Institute for Genomic Research Osal Rice Genome Annotation Database. Plant Physiol., 138, 18-26.
8. Whitelaw,C.A., Barbazuk,W.B., Pertea,G., Chan,A.P., Cheung,F., Lee,Y., Zheng,L., van Heeringen,S., Karamycheva,S., Bennetzen,J.L. et al. (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science, 302, 2118-2120.
9. Palmer,L.E., Rabinowicz,P.D., O'Shaughnessy,A.L., Balija,V.S., Nascimento,L.U., Dike,S., de la Bastide,M., Martienssen,R.A. and McCombie,W.R. (2003) Maize genome sequencing by methylation filtration. Science, 302, 2115-2117.
10. Fu,Y., Emrich,S.J., Guo,L., Wen,T-J., Ashlock,D.A., Aluru,S. and Schnable,P.S. (2005) Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes. Proc. Natl Acad. Sci. USA, 102, 12282-12287.
11. Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A., Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610.
12. Griffiths-Jones,S. (2004) The microRNA registry. Nucleic Acids Res., 32, D109-D111.
13. 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.
14. Dowell,R.D., Jokerst,R.M., Day,A., Eddy,S.R. and Stein,L. (2001) The distributed annotation system. BMC Bioinformatics, 2, 7.
15. Zuker,M. (2003) Predicting nucleic acid hybridization and melting profiles. Genome Inform., 14, 266-268.
16. Allen,E., Xie,Z., Gustafson,A.M. and Carrington,J.C. (2005) MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 121, 207-221.
17. Schwab,R., Palatnik,J., Riester,M., Schommer,C., Schmid,M. and Weigel,D. (2005) Specific effects of microRNAs on the plant transcriptome. Dev. Cell, 8, 517-527.