Argonaute--a database for gene regulation by mammalian microRNAs

Abstract

MicroRNAs (miRNAs) constitute a recently discovered class of small non-coding RNAs that regulate expression of target genes either by decreasing the stability of the target mRNA or by translational inhibition. They are involved in diverse processes, including cellular differentiation, proliferation and apoptosis. Recent evidence also suggests their importance for cancerogenesis. By far the most important model systems in cancer research are mammalian organisms. Thus, we decided to compile comprehensive information on mammalian miRNAs, their origin and regulated target genes in an exhaustive, curated database called Argonaute (). Argonaute collects latest information from both literature and other databases. In contrast to current databases on miRNAs like miRBase::Sequences, NONCODE or RNAdb, Argonaute hosts additional information on the origin of an miRNA, i.e. in which host gene it is encoded, its expression in different tissues and its known or proposed function, its potential target genes including Gene Ontology annotation, as well as miRNA families and proteins known to be involved in miRNA processing. Additionally, target genes are linked to an information retrieval system that provides comprehensive information from sequence databases and a simultaneous search of MEDLINE with all synonyms of a given gene. The web interface allows the user to get information for a single or multiple miRNAs, either selected or uploaded through a text file. Argonaute currently has information on 839 miRNAs from human, mouse and rat.

Differential regulation of MicroRNA expression in irradiated and bystander cells

“…The miR 143 and miR 145 were also induced in bystander cells. The miR 143 regulates connective tissue growth factor and its expression correlates with adipocyte differentiation and carcinogenesis [44]. Altered expression of miR 145 and miR 155 was detected in lung cancers [45].…”

Integrated microRNA and mRNA expression profiling in a rat colon carcinogenesis model: effect of a chemo-protective diet

“…Separate core analyses were performed using microRNA and total mRNA datasets. The miRWalk (previously known as Argonuate) algorithm was used to predict the association of microRNAs with gene targets (63). Molecules from each dataset that met the 1.5-fold change cut-off and were associated with biological functions and/or diseases in the Ingenuity's Knowledge Base were used to generate networks.…”

miRDB: A microRNA target prediction and functional annotation database with a wiki interface

“…TarBase has a main focus of collecting and presenting experimentally validated miRNA targets (Sethupathy et al 2006). More comprehensive databases have also been developed recently, attempting to integrate target prediction results with other functional annotations (Hsu et al 2006;Shahi et al 2006;Chiromatzo et al 2007;Megraw et al 2007;Nam et al 2008). These databases usually include data from miRBase for miRNA sequences and Here, we describe a new database, which we called miRDB, for miRNA target prediction and functional annotation.…”