Results that are displayed on the Knowledge Portals, including bottom-line genetic associations, credible sets, epigenomic annotations, global enrichments, and more, are stored in the HuGeAMP BioIndex and may be queried via REST API. The results in the BioIndex are updated with each production release.
Multi disease clustering landing page content
Below are brief tutorials illustrating how to explore results using each of these modules:
The single gene lookup page combines results from multiple analyses. Methods for each analysis can be found here:
Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease.
Lu X, et al.
Nat Genet. 2017 Dec;49(12):1722-1730. doi: 10.1038/ng.3978.
Tutorial for the Differential Expression View
We conducted the differential expression analysis with the R package DESeq2. We first filtered for protein-coding genes with more than 10 counts in at least 14 samples (our smaller group size). Fourteen low-risk (LR) samples were compared to 16 high-risk (HR) samples adjusting for age, sex, and RNA-Seq batch. Cook’s distance was used to flag associations influenced by sample outliers.
The APOL1 Portal was created to facilitate sharing and secondary use of analyses and data related to APOL1 associated kidney disease in order to parallelize and accelerate discovery for this condition.