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:

• Differential Expression
• Genome-wide APOL1 Correlations
• Differential Co-expression

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.

Sample information
Normalized gene expression
Gene counts
README

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.

Tutorial for the Interactive App

• Gene set enrichment - Submodule B
• Gene set enrichment - Submodule C
• Gene set enrichment - Submodule D
• Gene set enrichment - Submodule E<