Faster access to tools from the T2DKP home page

We've rearranged some of the links on the Type 2 Diabetes Knowledge Portal home page, as a first step towards offering a central location for analysis tools. The previous link to the Variant Finder tool has been replaced by a link to the new Analysis modules page:

The new page, shown below, offers access to three analysis tools.

• The Interactive Manhattan plot allows you to choose a phenotype and view variant associations across the genome for that phenotype.  We've added phenotype selection options to both the Analysis modules page and the Manhattan plot page, making it easier to switch your view between phenotypes.  The default view on the Manhattan plot page shows the largest dataset for a phenotype, but when multiple datasets exist, you can select any one to display. For many datasets, LD clumping is available at several r² thresholds. Clumping reduces redundancy due to association signals from linked variants, pinpointing the most strongly associated variant in a group.

• The Variant Finder is a versatile tool that allows you to set multiple criteria (phenotype, p-value, size and direction of effect, and more) and retrieve the set of variants meeting those criteria.

• The Genetic Risk Score (GRS) module takes a set of 243 variants associated with T2D at genome-wide significance or better, as determined by Mahajan et al. in their DIAMANTE (European) study (Mahajan et al., Nat Genet. 2018 Nov;50(11):1505-1513), allows users to select a phenotype and dataset, and computes the p-value for association of the variant set with the selected phenotype. The interface offers two customizing options: the ability to edit the variants in the set, and the ability to filter the samples by multiple phenotypic criteria before running the analysis. The GRS module, which will be augmented and improved in the future, can potentially reveal relationships between phenotypes. 

The new Analysis Modules page will be the central access point for new analysis tools as they are developed, so check back often for updates!