Nucleic Acids Research, 2006, Vol. 34, Database issue D135–D139 doi:10.1093/nar/gkj135 miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes Paul W.C. Hsu 1 , Hsien-Da Huang1,2,*, Sheng-Da Hsu 1 , Li-Zen Lin1, Ann-Ping Tsou 3 , Ching-Ping Tseng2,4, Peter F. Stadler5, Stefan Washietl6 and Ivo L. Hofacker6 1Institute of Bioinformatics and 2Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan, ROC, 3Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan, ROC, 4Institute of Biochemical Engineering, National Chiao Tung University, Hsin-Chu 300, Taiwan, ROC, 5Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, Germany and 6Institute of Theoretical Chemistry, University of Vienna, Austria Received August 15, 2005; Revised October 17, 2005; Accepted October 27, 2005 ABSTRACT Recent work has demonstrated that microRNAs (miRNAs) are involved in critical biological processes by suppressing the translation of coding genes. This work develops an integrated database, miRNAMap, to store the known miRNA genes, the putative miRNA genes, the known miRNA targets and the putative miRNA targets. The known miRNA genes in four mam- malian genomes such as human, mouse, rat and dog are obtained from miRBase, and experimentally vali- dated miRNA targets are identified in a survey of the literature. Putative miRNA precursors were identified by RNAz, which is a non-coding RNA prediction tool based on comparative sequence analysis. The mature miRNA of the putative miRNA genes is accurately determined using a machine learning approach, mmiRNA. Then, miRanda was applied to predict the miRNA targets within the conserved regions in 30-UTR of the genes in the four mammalian genomes. The miRNAMap also provides the expression profiles of the known miRNAs, cross-species comparisons, gene annotations and cross-links to other biological databases. Both textual and graphical web interface are provided to facilitate the retrieval of data from the miRNAMap. The database is freely available at http:// mirnamap.mbc.nctu.edu.tw/. INTRODUCTION MicroRNAs (miRNAs) are small RNA molecules, which are 22 nt sequences that have an important role in the translational regulation and degradation of mRNA by the base’s pairing to the 30-untranslated regions (30-UTR) of the mRNAs. The miRNAs are derived from the precursor tran- scripts of 70–120 nt sequences, which fold to form as stem– loop structures, which are thought to be highly conserved in the evolution of genomes. Previous analyses have suggested that 1% of all human genes are miRNA genes, which regu- late the production of protein for 10% or more of all human coding genes (1). Ambros et al. developed a uniform system for the identi- ﬁcation and annotation of new microRNA in a range of organ- isms (2). The miRBase (3) supports the sequence and annotation of the published miRNA genes. Washietl et al. developed a fast and reliable method for identifying the non-coding RNA structures using comparative sequence anal- ysis (4), which can be incorporated into the proposed resource to identify the conserved miRNA precursors in the four mam- malian genomes. TargetScan (5), miRanda (1) and RNAhybrid (6) are three previously developed tools for determining the energetically most favorable hybridization sites of a small RNA to a large RNA. PicTar (7) is a computational method for identifying common targets of known miRNAs. Lu et al. developed an miRNA microarray to measure the expression proﬁles of all known miRNA in various normal tissues and tumors (8). The investigation of the roles of miRNAs in various research ﬁelds depends on having plentiful miRNAs and information about them. This work develops an integrated database, miRNAMap, of miRNA genes, miRNA targets and the relationships between the miRNAs and the miRNA targets. The known miRNA genes in four mammals—humans, mice, rats and dogs—are obtained from miRBase (3). Experi- mentally validated miRNA targets are identiﬁed by surveying the literature. The putative miRNA precursors conserved in the *To whom correspondence should be addressed: Tel: +886-3-5712121 Ext. 56952; Email: bryan@mail.nctu.edu.tw The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. 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