Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes
Fig 2
Schematic of the SNP Prioritization Pipeline.
Genomic coordinates of genetic variants, regulatory elements, 3D connectome, genes are input into step one of the SNP Prioritization Pipeline. The output from Step 1 are associated genetic variants—regulatory elements—genes, which together formed trios. List of the unique genetic variants, regulatory elements, and genes that participate in these trios are also outputted. The gene list from step 1 of the SNP Prioritization Pipeline can be used as input for Biomedical Data Commons queries. The trios generated in step 1 are used as input into step 2 of the SNP Prioritization Pipeline along with optional input cell type-specific gene expression data. The output is visualizations of gene regulatory networks and a ranked list of genetic variants and genes. Input and output data at each step of the pipeline is color coded by type of data: genetic variants (green), regulatory elements (blue), genes (gold), 3D connectome (black), gene expression data (magenta), gene regulatory networks (turquoise), and ranked list of genetic variants and genes (orange). Optional input data is denoted by grey text, grey outline of the input box, and grey input arrow. *denotes input data that is cell type-specific and needs to belong to the same cell type of interest throughout the pipeline.