example, miRNAs might contribute to cancer, miRNA- mediated tumorigenesis results from either down-regulation of tumor suppressor genes or up-regulation of oncogenes (16). Moreover, human miRNA genes are frequently located at fragile sites and genomic regions that are involved in cancer (17). The miRNAMap developed herein can support research in this area by combining the data obtained by comparative genomic hybridization (CGH) experiments, which provide information of the gain and loss chromosomal regions in tumor genomes. A user who is interested in particular extra- ordinary chromosomes can use miRNAMap to obtain miRNA information by querying the cytobands. Integrated analyses of the CGH data, the expression proﬁles of the coding genes and the miRNAMap data demonstrate that the miRNA genes and the miRNA targets potentially participate in the regulation of cancer cells and can be systematically identiﬁed for further experimental veriﬁcation. The database will be developed as follows. (i) It will be made to support miRNA annotations including miRNA genes and miRNA targets for other species and (ii) the miRNAMap data will be further analysed to support the miRNAs involved in the combinatorial control of the gene expression of the coding genes. AVAILABILITY The miRNAMap database will be continuously maintained and updated. The database is now freely available at http:// miRNAMap.mbc.nctu.edu.tw. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. ACKNOWLEDGEMENTS The authors would like to thank the National Science Council of the Republic of China for financially supporting this research under Contract No. NSC 94-2213-E-009-025. Funding to pay the Open Access publication charges for this article was pro- vided by National Science Council of the Republic of China. Conflict of interest statement. None declared. Nucleic Acids Research, 2006, Vol. 34, Database issue D139 REFERENCES 1. John,B., Enright,A.J., Aravin,A., Tuschl,T., Sander,C. and Marks,D.S. (2004) Human MicroRNA targets. PLoS Biol., 2, e363. 2. Ambros,V., Bartel,B., Bartel,D.P., Burge,C.B., Carrington,J.C., Chen,X., Dreyfuss,G., Eddy,S.R., Griffiths-Jones,S., Marshall,M. et al. (2003) A uniform system for microRNA annotation. RNA, 9, 277–279. 3. Griffiths-Jones,S. (2004) The microRNA Registry. Nucleic Acids Res., 32, D109–D111. 4. Washietl,S., Hofacker,I.L. and Stadler,P.F. (2005) Fast and reliable prediction of noncoding RNAs. Proc. Natl Acad. Sci. USA, 102, 2454–2459. 5. Lewis,B.P., Shih,I.H., Jones-Rhoades,M.W., Bartel,D.P. and Burge,C.B. (2003) Prediction of mammalian microRNA targets. Cell, 115, 787–798. 6. Rehmsmeier,M., Steffen,P., Hochsmann,M. and Giegerich,R. (2004) Fast and effective prediction of microRNA/target duplexes. RNA, 10, 1507–1517. 7. 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. Nat. Genet., 37, 495–500. 8. Lu,J., Getz,G., Miska,E.A., Alvarez-Saavedra,E., Lamb,J., Peck,D., Sweet-Cordero,A., Ebert,B.L., Mak,R.H., Ferrando,A.A. et al. (2005) MicroRNA expression profiles classify human cancers. Nature, 435, 834–838. 9. Karolchik,D., Baertsch,R., Diekhans,M., Furey,T.S., Hinrichs,A., Lu,Y.T., Roskin,K.M., Schwartz,M., Sugnet,C.W., Thomas,D.J. et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res., 31, 51–54. 10. Hubbard,T., Andrews,D., Caccamo,M., Cameron,G., Chen,Y., Clamp,M., Clarke,L., Coates,G., Cox,T., Cunningham,F. et al. (2005) Ensembl 2005. Nucleic Acids Res., 33, D447–D453. 11. Harris,M.A., Clark,J., Ireland,A., Lomax,J., Ashburner,M., Foulger,R., Eilbeck,K., Lewis,S., Marshall,B., Mungall,C. et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 32, D258–D261. 12. Cotton,R.G., McKusick,V. and Scriver,C.R. (1998) The HUGO Mutation Database Initiative. Science, 279, 10–11. 13. Hofacker,I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429–3431. 14. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406–3415. 15. 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. 16. Caldas,C. and Brenton,J.D. (2005) Sizing up miRNAs as cancer genes. Nat. Med., 11, 712–714. 17. Calin,G.A., Sevignani,C., Dumitru,C.D., Hyslop,T., Noch,E., Yendamuri,S., Shimizu,M., Rattan,S., Bullrich,F., Negrini,M. et al. (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl Acad. Sci. USA, 101, 2999–3004.