MiRTargetLink--miRNAs, Genes and Interaction Networks

Abstract

Information on miRNA targeting genes is growing rapidly. For high-throughput experiments, but also for targeted analyses of few genes or miRNAs, easy analysis with concise representation of results facilitates the work of life scientists. We developed miRTargetLink, a tool for automating respective analysis procedures that are frequently applied. Input of the web-based solution is either a single gene or single miRNA, but also sets of genes or miRNAs, can be entered. Validated and predicted targets are extracted from databases and an interaction network is presented. Users can select whether predicted targets, experimentally validated targets with strong or weak evidence, or combinations of those are considered. Central genes or miRNAs are highlighted and users can navigate through the network interactively. To discover the most relevant biochemical processes influenced by the target network, gene set analysis and miRNA set analysis are integrated. As a showcase for miRTargetLink, we analyze targets of five cardiac miRNAs. miRTargetLink is freely available without restrictions at www.ccb.uni-saarland.de/mirtargetlink.

Keywords: genes; interaction networks; miRNAs; miRTargetkLink.

Figure 1

Single miRNA mode for miR-107: The central node is the miRNA, surrounded by validated targets with strong evidence (green), weak evidence (blue), and predicted targets (yellow). In the second representation predicted edges and in the third weak evidence edges are removed. The final representation is gene-centric for one of the target gens of miR-107, CAV1.

Figure 2

Multi-miRNA mode. For five cardio miRNAs, the network of genes that are targeted by at least two miRNAs (experimental evidence) is shown. Edge color indicates the number of miRNA-target interactions for the miRNAs that are start nodes of the edges. The second representation highlights the genes that are supported by strong evidence experiments.