D162 Nucleic Acids Research, 2011, Vol. 39, Database issue Figure 3. The three different types of associations in the association analysis module. Depending on the data category, (A) miRSA, (B) GSA and (C) miRPA. user-deﬁned gene/miRNA sets may be saved on the system, which can be retrieved later for further analysis. CONCLUSION The miRGator v2.0 integrates human miRNA-related ex- pression patterns under various disease and perturbation conditions. The system is designed to facilitate functional investigation of miRNAs by integrating various evidences of miRNA targets and by revealing non-canonical associ- ations among miRNAs, diseases, perturbations and user- deﬁned gene/miRNA sets. FUNDING GIST Systems Biology Infrastructure Establishment Grant (2010) through Ewha Research Center for Systems Biology (ERCSB); Biogreen 21 Program of the Korean Rural Development Administration (20070401034010); National Core Research Center (NCRC) program (R15-2006-020) of the KOSEF funded by the MEST. Funding for open access charge: GIST Systems Biology Infrastructure Establishment Grant (2010) through Ewha Research Center for Systems Biology (ERCSB). REFERENCES 1. Bartel,D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215–233. 2. Bartel,D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281–297. 3. Friedman,R.C., Farh,K.K., Burge,C.B. and Bartel,D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92–105. 4. Kertesz,M., Iovino,N., Unnerstall,U., Gaul,U. and Segal,E. (2007) The role of site accessibility in microRNA target recognition. Nat. Genet., 39, 1278–1284. 5. Betel,D., Wilson,M., Gabow,A., Marks,D.S. and Sander,C. (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res., 36, D149–D153. 6. 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. 7. Lee,I., Ajay,S.S., Yook,J.I., Kim,H.S., Hong,S.H., Kim,N.H., Dhanasekaran,S.M., Chinnaiyan,A.M. and Athey,B.D. (2009) New class of microRNA targets containing simultaneous 50-UTR and 30-UTR interaction sites. Genome Res., 19, 1175–1183. 8. Ruepp,A., Kowarsch,A., Schmidl,D., Buggenthin,F., Brauner,B., Dunger,I., Fobo,G., Frishman,G., Montrone,C. and Theis,F.J. (2010) PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol., 11, R6. 9. Jiang,Q., Wang,Y., Hao,Y., Juan,L., Teng,M., Zhang,X., Li,M., Wang,G. and Liu,Y. (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res., 37, D98–D104. 10. Ulitsky,I., Laurent,L.C. and Shamir,R. (2010) Towards computational prediction of microRNA function and activity. Nucleic Acids Res., 38, e160. 11. Nam,S., Li,M., Choi,K., Balch,C., Kim,S. and Nephew,K.P. (2009) MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res., 37, W356–W362. 12. Sales,G., Coppe,A., Bisognin,A., Biasiolo,M., Bortoluzzi,S. and Romualdi,C. MAGIA, a web-based tool for miRNA and genes integrated analysis. Nucleic Acids Res., 38(Suppl.), W352–W359. 13. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the uniﬁcation of biology. The Gene Ontology Consortium. Nature Genet., 25, 25–29. 14. Kanehisa,M., Goto,S., Hattori,M., Aoki-Kinoshita,K.F., Itoh,M., Kawashima,S., Katayama,T., Araki,M. and Hirakawa,M. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res., 34, D354–357. 15. Barrett,T., Troup,D.B., Wilhite,S.E., Ledoux,P., Rudnev,D., Evangelista,C., Kim,I.F., Soboleva,A., Tomashevsky,M., Marshall,K.A. et al. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res., 37, D885–D890. 16. Parkinson,H., Kapushesky,M., Kolesnikov,N., Rustici,G., Shojatalab,M., Abeygunawardena,N., Berube,H., Dylag,M., Emam,I., Farne,A. et al. (2009) ArrayExpress update––from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res., 37, D868–D872. 17. Smyth,G.K. and Speed,T. (2003) Normalization of cDNA microarray data. Methods, 31, 265–273. 18. Amberger,J., Bocchini,C.A., Scott,A.F. and Hamosh,A. (2009) McKusick’s Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res., 37, D793–D796. 19. Becker,K.G., Barnes,K.C., Bright,T.J. and Wang,S.A. (2004) The genetic association database. Nature Genet., 36, 431–432.