show me some regulation...

Regul@tionSpotter

Tutorial

In our tutorial, we will exemplarily lead you through the analysis of sequencing results with help of RegulationSpotter.

In our example, a patient presenting with portal and hepatic vein thrombosis and seizures is suspected to suffer from a glycosylphosphatidylinositol deficiency. A panel sequencing with all genes known to cause human hereditary diseases including up- and downstream extragenic regions was carried out. To improve the chances of finding the causative mutation, candidate genes were determined based on the condition of the presenting patient and the sequencing results were filtered to exclude variants located in other genes. The candidate genes for our case were: PIGV, PIGN, PIGA, PIGL, PIGO, PIGT, PGAP2, PGAP1, PGAP3, PIGW, PIGY, PIGG.

In our hypothetical case, we have already analysed intragenic variants in the list of candidate genes but did not find a convincing disease-causing mutation. Hence, we assume that the disease is caused by a mutation in a regulatory region and decide to examine our vcf with RegulationSpotter.

Please follow the instructions to analyse the example vcf file with RegulationSpotter.

Let's get started

vcf file

To start with our tutorial, please go to the RegulationSpotter start page. Here, you can find the vcf file (sample file). Please save it on your computer and then upload it to RegulationSpotter. Alternatively, you can also get the vcf file here.

In this file, you can find variants located in the candidate genes. Additionally, there are some regulatory variants as well. Most of this genetic variation is harmless, but we expect one of the alterations to be causative for the disease.

Analysis settings

When uploading the vcf file, you can specify a number of settings for the analysis. For our purposes, please stick with the default settings.

Analyse the following regions or genes

In a typical case, you might end up with a rather large vfc file, especially if you are looking at entire exomes or genomes. Therefore, you would usually start with rather stringent filtering options.
In our tutorial, the vcf file is rather small to decrease waiting times for you. However, it still makes sense to restrict the analysis to the list of candidate genes.
Thus, please select analyse custom genes (select to enter) and enter our candidate genes:
PIGV, PIGN, PIGA, PIGL, PIGO, PIGT, PGAP2, PGAP1, PGAP3, PIGW, PIGY, PIGG, PIGM


If you want to know more about the settings options, please refer to our documentation.

Once you are done, just hit "submit" and wait for RegulationSpotter to work on your file.

Synopsis and display settings

RegulationSpotter will lead you now to its first landing page. On the left side, you will find a synopsis of your vcf file. The center of the page allows you to filter and sort your results for display. For detailed information on this page, please also refer to our documentation.

If you are planning to access your project later on, please record your project ID. This enables you to just enter it whenever you want to have a look at your results again.

Note: Please DO NOT change or delete this ID as RegulationSpotter requires it!

Display settings

Here, you can filter and sort your results for display. In a real-life case, you would most likely start with a strict filter to avoid being swamped by your data. Even though our tutorial set is rather small, we should still hide extragenic variants without annotation, so please select this option.

As we suspect that our causative alteration is located in a regulatory region, we are interested in variants with a high likelihood for regulatory location.
Therefore, please select 'sort by effect, chromosome, position'.
When you are done, just hit display to get your results.

Results

RegulationSpotter first gives you an overview of its findings. In the left, text-based, part you can find all sort of useful information about the variant, such as chromosomal position, reference and alternative allele, and connected gene. The rest of the summary is a colour-coded table indicating different types of regulatory features which might be affected. Further information on the summary table can be found in our documentation.

As we suspect that the causative mutation is located in a regulatory region, first of all we now focus on variants which are most likely located in a regulatory region. This is indicated in the likely effect column.
RegulationSpotter calculates a probability score, which indicates the likelihood of a variant to be located in a regulatory region. To do this, RegulationSpotter compiles and integrates all the information or annotations it can find about the location of a variant. The higher the score, the more likely is a functional relevance of a region. Use the following parameters to sort the results We can now click on each of these variants to get more information on the regulatory region. Please refer to our documentation for detailed information on the RegulationSpotter's results display.

Contact

In case you discover bugs, have suggestions or questions, please write an e-mail to
Jana Marie Schwarz (jana-marie.schwarz AT charite.de) or to
Dominik Seelow
(dominik.seelow AT charite.de).
We also appreciate hearing about your general experiences using MutationTaster.