CD4 and tuberculosis: While differential expression analysis between TB and controls did not identify any study-wide significant genes at FDR < 5% (i.e. accounting for 64,057 total tests across 31 cell clusters), gene set analysis using the full spectrum of test statistics 28 identified a study-wide significant upregulation in TB cases of ‘cellular response to interferon-gamma’ in the CD4/8+ PD-1+TIGIT+ cluster, and a handful of other genesets in other T-cell clusters (Figure 3G).