How to use MMP
Last updated
Last updated
See a tutorial video on how to use the Multiple Manhattan Plot (MMP) tool from the 27th September 2022 Users' Meeting video.
See also a presentation of New FinGen tools and their application to example diseases from User's meeting 28th March 2023 recording (at 25min 23sec) including usage of Multiple Manhattan Plot tool.
Navigate to https://geneviz.aalto.fi/MMP/dashboard/. Click Upload your dataset and select your MMP input file.
Select Pos for Position, x chrom for Chromosome, Ref for Reference, Alt for Alternative, and Af_alt for Allele frequency.
Select p- and beta value pairs for GWASs included in the Multiple Manhattan plot. Import the endpoint's p-values and beta to P-value and Beta boxes by clicking their name in the Key selector. The MMP will suggest suitable variables with red highlighting. Endpoints will show in the Multiple Manhattan plot in the same order as they are selected in. Once ready, Click Confirm keys.
The genome view page will open in Chart mode. Resolution within Chromosome's views can be adjusted from the upper right corner by clicking the arrows up or down or by typing in the target resolution to the resolution field. Log p-values are shown in three colors. The thresholds for the colors are shown on the left. The threshold values are adjustable by dragging and dropping the white dots. Note that the limits for the highest p-values are already selected when the input file is prepared.
Click any of the chromosome blocks in the Genome view to zoom into a Chromosome view. Resolution and p-values are adjustable also on the Chromosome view.
Select table mode from the top bar of the MMP page to open the Top associations' view. The Top associations' view shows top associations with the smallest p-values for the selected GWAS. The selected GWAS is highlighted in yellow. Click the name of the GWAS to change the view to that GWAS. By default 10 top associations are shown. To see more click Expand table. The table can be filtered by chromosomes from the Filter table button and then selecting the chromosome number to be shown.
The Slot view is accessible from the Chromosome view and Top Associations view. On the Chromosome view, click any position to zoom in on the Slot view. The Slot view will show compared GWASs for the selected slot with min p-values shown. Gene names, regions, and directions are shown on top of the Slot view. The start and end positions for the region are shown.
On the Top Associations view, click one association to open the Slot view.
To zoom into Locus view, click a position from the Slot view. The Locus view will open under the Slot view. The Locus view shows positions at the x-axis and log p-values at the y-axis colored by the GWAS run. Click one position to select it. On the left chromosome, position, reference allele, alternative allele, coding variants, genes, and allele frequency are shown for the selected position.
