miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes

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 mammalian genomes such as human, mouse, rat and dog are obtained from miRBase, and experimentally validated 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 3′-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 .

The role of microRNAs (miRNA) in circadian rhythmicity

“…The free energy ΔG predicted for this structure is −30.2 kcal/mole. Pre-miRNA sequence was obtained from miRNAMap (Hsu et al 2006) (http://mirnamap.mbc.nctu.edu.tw) and the structure was derived using the mfold algorithm (Zuker 2003) available at (http://mfold.bioinfo.rpi.edu/cgi-bin/rna-form1.cgi).…”

An Array-Based Analysis of MicroRNA Expression Comparing Matched Frozen and Formalin-Fixed Paraffin-Embedded Human Tissue Samples

“…Currently, it is estimated that up to 30% of protein coding genes might be regulated by miRNAs at the posttranscriptional level. 4,5 Recent studies have demonstrated that miRNAs regulate various cell functions, including cell proliferation, differentiation, death, stress resistance, and fat metabolism. 4 -6 Accordingly, it is reasonable to suggest that abnormal miRNAs expression is likely to contribute to human disease, including cancer.…”

MicroRNAs in hereditary and sporadic premature aging syndromes and other laminopathies

“…miRNA genes are present in intergenic regions with an independent promoter (52%), in introns (40%), or less frequently in exons (8%). In these last two cases, the expression of the miRNA is linked to transcription of the host gene (Hsu et al., 2006; Rodriguez, Griffiths‐Jones, Ashurst & Bradley, 2004). To become mature, miRNAs need to undergo several post‐transcriptional modifications.…”