TY - JOUR T1 - miRGen 2.0: a database of microRNA genomic information and regulation. JF - Nucleic Acids Res Y1 - 2010 A1 - Alexiou, Panagiotis A1 - Vergoulis, Thanasis A1 - Gleditzsch, Martin A1 - Prekas, George A1 - Dalamagas, Theodore A1 - Megraw, Molly A1 - Grosse, Ivo A1 - Sellis, Timos A1 - Hatzigeorgiou, Artemis G KW - 3' Untranslated Regions KW - Algorithms KW - Animals KW - Cell Line, Tumor KW - Computational Biology KW - Databases, Genetic KW - Databases, Nucleic Acid KW - Humans KW - Information Storage and Retrieval KW - Internet KW - Mice KW - MicroRNAs KW - Polymorphism, Single Nucleotide KW - Software KW - Transcription Factors AB -

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/.

VL - 38 IS - Database issue ER - TY - JOUR T1 - A guide through present computational approaches for the identification of mammalian microRNA targets. JF - Nat Methods Y1 - 2006 A1 - Sethupathy, Praveen A1 - Megraw, Molly A1 - Hatzigeorgiou, Artemis G KW - 3' Untranslated Regions KW - 5' Untranslated Regions KW - Animals KW - Computational Biology KW - Gene Targeting KW - Humans KW - MicroRNAs KW - Predictive Value of Tests KW - RNA, Messenger KW - Sensitivity and Specificity KW - Software AB -

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.

VL - 3 IS - 11 ER -