Differential pathway expression analysis in proliferating HIVneg and HIVpos GC-Tfh cells.

We used Gene Set Variation Analysis (GSVA) to determine the biological characterization, statistical significance and differences in selected databases. We performed enrichment analyses using Ingenuity Pathway Analysis (IPA) gene sets to determine the profile of GC-Tfh cell proliferation in the context of HIV or a non-HIV environment. We generated checkerboard plots representing the top lists of enriched pathways in the DEGs specific to proliferating GC-Tfh cells in the HIVneg and HIVpos contexts (Fig 4A and 4B). The top enriched pathway list in HIVneg cells is shown in the first Table sheet while the top enriched pathway list in the HIVpos cells is shown in the second Table sheet. Pathways are listed with their log2-fold change (logFC) and their nominal p-value. Statistical significance was considered with nominal p-values p (XLSX)