The microRNA.org resource: targets and expression

Abstract

MicroRNA.org (http://www.microrna.org) is a comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. Using an improved graphical interface, a user can explore (i) the set of genes that are potentially regulated by a particular microRNA, (ii) the implied cooperativity of multiple microRNAs on a particular mRNA and (iii) microRNA expression profiles in various tissues. To facilitate future updates and development, the microRNA.org database structure and software architecture is flexibly designed to incorporate new expression and target discoveries. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation.

Figure 1.

Scientific use cases for exploring microRNA target predictions. In case A, users search for the ‘predicted target genes of a given microRNA’. In the gene list view, an expandable display shows a schematic view of the microRNA target sites on a selected target gene. A selected target gene is also hyperlinked to a detailed view of the microRNA-binding sites in the 3′-UTR, including exact nucleotide positions, microRNA:mRNA duplex, alignment score and conservation as well as the ranked list of the binding sites. Similarly, in case B, users can reach the detailed target-sites-on-sequence view by ‘querying by gene name’.

Figure 2.

Scientific use cases for exploring microRNA expression. In case C, users can select to view the ‘tissue expression profile of a microRNA’. Additional microRNAs can be incorporated into the graph from the list of microRNAs at the top of the view. Additional tissues can also be added or removed by selection from the list on the left. In the parallel instance D, users can select to ‘view the microRNA expression profile of a tissue (or a list of tissues)’. By analogous selections, users can incorporate additional microRNAs and tissues into the view from their respective lists. In both use cases, the data can be visualized as a heat map: vertical and horizontal axes represent tissues and microRNAs and colors represent microRNA expression levels. Additionally, in all views microRNAs are linked to their target view.