fRNAdb: A platform for mining/annotating functional RNA candidates from non-coding RNA sequences

Nucleic Acids Research

Volumn 35, Issue SUPPL. 1, 2007, Pages

  Kin, Taishin ^a   Yamada, Kouichirou ^c   Terai, Goro ^b   Okida, Hiroaki ^b   Yoshinari, Yasuhiko ^d   Ono, Yukiteru ^c   Kojima, Aya ^b   Kimura, Yuki ^c   Komori, Takashi ^b   Asai, Kiyoshi ^a,e  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b INTEC Web and Genome Informatics Corporation   (Japan)

^c Information and Mathematics Science Laboratory Inc   (Japan)

^d MITSUBISHI RESEARCH INSTITUTE   (Japan)

^e UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; UNTRANSLATED RNA;

ACCESS TO INFORMATION; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; EXPRESSED SEQUENCE TAG; FUNCTIONAL RNA DATABASE; GENETIC DATABASE; INFORMATION PROCESSING; INTERNET; NONCODE DATABASE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA DATABASE; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSCRIPTION; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; VALIDATION STUDY;

BASE SEQUENCE; DATABASES, NUCLEIC ACID; GENOMICS; INTERNET; MICRORNAS; RNA, MESSENGER; RNA, UNTRANSLATED; USER-COMPUTER INTERFACE;

EID: 33846056835     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl837     Document Type: Article

References (20)

1. Imanishi,T., Itho,T., Suzuki,Y., O'Donovan,C., Fukuchi,S., Koyanagi,K.O., Barrero,R.A., Tamura,T., Yamaguchi-Kabata,Y., Tanino,M. et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol., 2, 856-875.
2. Liu,C., Bai,B., Skogerbo,G., Cai,L., Deng,W., Zhang,Y., Bu,D., Zhao,Y. and Chen,R. (2005) NONCODE: An integrated knowledge database of non-coding RNAs. Nucleic Acids Res., 33, D112-D115.
3. Pang,K.C., Stephen,S., Engstrom,P.G., Tajul-Arifin,K., Chen,W., Wahlestedt,C., Lenhard,B., Hayashizaki,Y. and Mattick,J.S. (2005) RNAdb - a comprehensive mammalian noncoding RNA database. Nucleic Acids Res., 33, D125-D130.
4. Hinrichs,A.S., Karolchik,D., Baertsch,R., Barber,G.P., Bejerano,G., Clawson,H., Diekhans,M., Furey,T.S., Harte,R.A., Hsu,F. et al. (2006) The UCSC Genome Browser Database: Update 2006. Nucleic Acids Res., 34, D590-D598.
5. Cheng,J., Kapranov,P., Drenkow,J., Dike,S., Brubaker,S., Patel,S., Long,J., Stern,D., Tammana,H., Helt,G. et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308, 1149-1154.
6. Szymanski,M., Erdmann,V.A. and Barciszewski,J. (2003) Noncoding regulatory RNAs database. Nucleic Acids Res., 31, 429-431.
7. Griffiths-Jones,S. (2006) miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 34, D140-D144.
8. Hsu,P.W., Huang,H.D., Hsu,S.D., Lin,L.Z., Tsou,A.P., Tseng,C.P., Stadler,P.F., Washiel,S. and Hofacker,I.L. (2006) miRNAMap: Genomic maps of microRNA genes and their target genes in mammalian genome. Nucleic Acids Res., 34, D135-D139.
9. Berezikov,E., Guryev,V., van de Belt,J., Wienholds,E., Plasterk,R.H. and Cuppen,E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell, 120, 21-24.
10. Sethupathy,P., Corda,B. and Hatzigeorgiou,A.G. (2006) TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA, 12, 192-197.
11. Kuger,J. and Rehmsmeier,M. (2006) RNAhybrid: MicroRNA target prediction easy, fast and flexible. Nucleic Acids Res., 34, W451-W454.
12. Krek,A., Grun,D., Poy,M.N., Wolf,R., Rosenberg,L, Epstein,E.J., MacMenamin,P., da Piedade,I., Gunsalus,K.C., Stoffel,M. et al. (2005) Combinatorial microRNA target predictions. Nature Genet., 37, 495-500.
13. Lewis,B.P., Burge,C.B. and Bartel,D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
14. Pollard,K.S., Salama,S.R., Lambert,N., Lambot,M.A., Coppens,S., Pedersen,J.S., Katzman,S., King,B., Onodera,C., Siepel,A. et al. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature, 443, 167-172.
15. Washietl,S., Hofacker,I.L., Lukasser,M., Huttenhofer,A. and Stadler,P.F. (2005) Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat. Biotechnol., 23, 1383-1390.
16. Furuno,M., Pang,K.C., Ninomiya,N., Fukuda,S., Frith,M.C., Bult,C., Kai,C., Kawai,J., Carninci,P., Hayashizaki,Y. et al. (2006) Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet., 2, e37.
17. Chen,J., Sun,M., Kent,W.J., Huang,X., Xie,H., Wang,W., Zhou,G., Shi,R.Z. and Rowley,J.D. (2004) Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res., 32, 4812-4820.
18. Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
19. Bejerano,G., Pheasant,M., Makunin,I., Stephen,S., Kent,W.J., Mattick,J.S. and Haussler,D. (2004) Ultraconserved elements in the human genome. Science, 304, 1321-1325.
20. Simons,C., Pheasant,M., Makunin,I.V. and Mattick,J.S. (2005) Transposon-free regions in mammalian genome. Genome Res., 16, 164-172.