D138 Nucleic Acids Research, 2006, Vol. 34, Database issue Figure 2. Interface of the miRNA genes in miRNAMap. The expression proﬁles of the miRNAs are helpful in elu- cidating the regulatory roles of the miRNAs. Lu et al. con- structed the miRNA microarray to elucidate the gene expression proﬁles in various normal tissue and tumors (8). The gene expression data for known miRNAs were integrated into the miRNAMap to determine the tissue-speciﬁcity of the known miRNAs. INTERFACE Various query interfaces and graphical visualization pages were implemented to facilitate access to data and further analyses to support research on miRNA. The miRNAMap provides two modes for browsing the miRNA information—the miRNA genes browser and the miRNA tar- get browser. As presented in Figure 2, the chromosomal view facilitates the browsing of the miRNA genes. The miRNA gene page shows the sequence, mature miRNA, genomic loca- tion, relevant citations from the literature, gene annotations, tissue-speciﬁcity and conserved sequences obtained from the UCSC Genome Browser (9). In particular, the diagram reveal- ing the stem–loop RNA structure of the miRNA precursor, which is folded using RNAfold (13), is generated graphically by mfold (14). Figure S1 (Supplementary Data) presents a graphical visu- alization tool that is used to present the miRNAs that can target a gene transcript. All the miRNA target sites are also provided in text format: the text states the genomic locations of the target sites, the MFE of the miRNAs, the sequences of the target sites and the alignment of the hybridization structures. Users can change the MFE threshold and score threshold to ﬁlter the miRNA targets of interest. The miRNAMap provides various search criteria for access- ing the data, including keyword, accession of the miRNAs, chromosomal locations and names of miRNA target genes. In particular, searching the database by submitting a group of genes helps users elucidate the roles of miRNAs in various gene groupings and to explicate the cooperative or combina- torial control of gene expression by a group of miRNAs (15). Users can also submit gene groups or families using HGNC annotations (12). The tutorial documentation on the miRNAMap website describes in detail the usage of miRNAMap web interfaces. CONCLUSIONS An integrated database for miRNAs, miRNAMap, was estab- lished to compile the known miRNAs, the putative miRNAs, the miRNA targets and the regulatory relationships between the miRNAs and the coding genes in humans, mice, rats and dogs. The authors hope that this database can provide sufﬁ- cient information to support any miRNAs-related works. For