%0 Journal Article %J Nucleic Acids Res %D 2010 %T miRGen 2.0: a database of microRNA genomic information and regulation. %A Alexiou, Panagiotis %A Vergoulis, Thanasis %A Gleditzsch, Martin %A Prekas, George %A Dalamagas, Theodore %A Megraw, Molly %A Grosse, Ivo %A Sellis, Timos %A Hatzigeorgiou, Artemis G %K 3' Untranslated Regions %K Algorithms %K Animals %K Cell Line, Tumor %K Computational Biology %K Databases, Genetic %K Databases, Nucleic Acid %K Humans %K Information Storage and Retrieval %K Internet %K Mice %K MicroRNAs %K Polymorphism, Single Nucleotide %K Software %K Transcription Factors %X

MicroRNAs are small, non-protein coding RNA molecules known to regulate the expression of genes by binding to the 3'UTR region of mRNAs. MicroRNAs are produced from longer transcripts which can code for more than one mature miRNAs. miRGen 2.0 is a database that aims to provide comprehensive information about the position of human and mouse microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both predicted and experimentally supported data. Expression profiles of microRNAs in several tissues and cell lines, single nucleotide polymorphism locations, microRNA target prediction on protein coding genes and mapping of miRNA targets of co-regulated miRNAs on biological pathways are also integrated into the database and user interface. The miRGen database will be continuously maintained and freely available at http://www.microrna.gr/mirgen/.

%B Nucleic Acids Res %V 38 %P D137-41 %8 2010 Jan %G eng %N Database issue %R 10.1093/nar/gkp888 %0 Journal Article %J Nat Methods %D 2006 %T A guide through present computational approaches for the identification of mammalian microRNA targets. %A Sethupathy, Praveen %A Megraw, Molly %A Hatzigeorgiou, Artemis G %K 3' Untranslated Regions %K 5' Untranslated Regions %K Animals %K Computational Biology %K Gene Targeting %K Humans %K MicroRNAs %K Predictive Value of Tests %K RNA, Messenger %K Sensitivity and Specificity %K Software %X

Computational microRNA (miRNA) target prediction is a field in flux. Here we present a guide through five widely used mammalian target prediction programs. We include an analysis of the performance of these individual programs and of various combinations of these programs. For this analysis we compiled several benchmark data sets of experimentally supported miRNA-target gene interactions. Based on the results, we provide a discussion on the status of target prediction and also suggest a stepwise approach toward predicting and selecting miRNA targets for experimental testing.

%B Nat Methods %V 3 %P 881-6 %8 2006 Nov %G eng %N 11 %R 10.1038/nmeth954