Yum, beautiful regulatory variants to spot...



RegulationSpotter: User-friendly interpretation of extragenic DNA sequence variants

RegulationSpotter is a web-based tool for the interpretation of extragenic DNA variants. It does not require any bioinformatics skills and is directly aimed at clinicians and researchers. It facilitates translational research projects without advanced bioinformatics knowledge but with valuable expertise about phenotypes and genes, a key point in exploiting Whole Genome Sequencing (WGS) data to identify disease mutations.

The tool integrates data from various sources to show whether a variant lies within a regulatory region and has the potential to impair gene expression. RegulationSpotter allows the user to learn about their variants of interest in a convenient fashion. It visualizes the regulatory importance of a variant and hence enables researchers to make educated choices about the alterations encountered in WGS data.

Work flow

To allow comprehensive analyses, RegulationSpotter accepts both intragenic and extragenic alterations: Intragenic variants, coding or non-coding, are handled by our popular program MutationTaster, while extragenic variants get assessed by RegulationSpotter directly. There are two ways to get started with RegulationSpotter: It reads variants from standard VCF files and maps them to genes and / or regulatory elements associated with genes. Moreover users can also simply query single variants. Have a look at RegulationSpotter's workflow below. (Fig. 1)

RegulationSpotter workflow
Fig. 1: A depiction of RegulationSpotter's workflow.
The program's comprehensive output combines a summary table with a graphical matrix depicting key aspects of all analysed variants. The software also provides the option to show more detailed information for every single variant by following the provided hyperlinks.

The intuitive design allows to get a quick yet thorough understanding of a variant's localisation and its possible role in gene regulation. Variants can be sorted by different parameters, such as phylogenetic conservation, CADD scores, or the RegulationSpotter Xscore. This score reflects the amount of available evidence that a variant is localised in a regulatory region and might impair its proper function. The analysis can be restricted to variants located in candidate genes, their promoters, and cis-modifiers.

To get started with RegulationSpotter, have a look at our tutorial. Feel free to contact us if you encounter any problems.