Tutorial for the Genome-Wide APOL1 Correlations View
We calculated Spearman correlations between APOL1 expression and normalized expression for each gene in high-risk (HR), low-risk (LR), and normal samples. To compare HR to LR correlations, we transformed the correlations using the Fisher Z-transformation.
Gene expression was variance stabilized (DESeq2), batch corrected (Combat), and quantile normalized. Gene expression was not normalized by gene length, so while we can compare correlation trends, we cannot compare expression levels of different genes.
To identify cellular processes and pathways correlated with APOL1 expression, we input sorted APOL1 correlations into Webgestalt GSEA. Results for the HR and LR analysis are linked below.
Significant annotations from both HR and LR GSEAs are highlighted in the figure below. Annotations to the right of the hashed line indicate gene sets enriched among genes positively correlated with APOL1 in both the high-risk and low-risk groups. Annotations to the left of the hashed line indicate gene sets with significant enrichment in both analyses, but in opposite directions -- Genes within these annotations were negatively correlated with low-risk APOL1 expression and positively correlated with high-risk APOL1 expression.
GSEA analysis results
- Low-risk GO: Biologic Process
- Low-risk GO: Cellular Compartment
- Low-risk GO: Molecular Function
- Low-risk KEGG
- Low-risk Panther
- Low-risk Reactome
- Low-risk Wikipathways
- High-risk GO: Biologic Process
- High-risk GO: Cellular Compartment
- High-risk GO: Molecular Function
- High-risk KEGG
- High-risk Panther
- High-risk Reactome
- High-risk Wikipathways
Column descriptions
Gene Symbol: The gene symbol is hyperlinked to the gene page, which provides information for this gene from all analyses.
Gene Name: The descriptive name of the gene product.
Ensembl Gene ID: The Ensembl ID is hyperlinked to the gene page, which provides information for this gene from all analyses.
View Plot: Mouse over to see a scatter plot and linear fit of APOL1 and each gene stratified by LR and HR.
Low-risk Correlation: Spearman correlation with APOL1 among the low-risk samples.
Low-risk P-value: Spearman correlation p-value for low-risk correlation; not adjusted for multiple testing.
High-risk Correlation: Spearman correlation with APOL1 among the high-risk samples.
High-risk P-value: Spearman correlation p-value for high-risk correlation; not adjusted for multiple testing.
|Z-score| - HR vs LR Correlation Difference: Absolute value of z-score for the test of correlation differences between HR and LR. Z-scores larger than 1.96 are significant at a 5% level of significance.
Normal Tissue Correlation: Spearman correlation with APOL1 among the normal samples. The notation "-99" indicates genes removed due to low counts.
Normal Tissue P-value: Spearman correlation p-value for normal sample correlation; not adjusted for multiple testing. The notation "-99" indicates genes removed due to low counts.