Fig 3A outlines some of these gene sets. Notably, the top downregulated gene sets include 97/186 (52%) genes previously associated with HIV-1 infection, which we refer to here as the HIV-1 ‘reactome’ (Fig 3B). A substantial fraction (23/97; 24%) of these HIV-1 reactome genes are associated with mRNA processing, but genes linked to the proteasome, transcription, vesicle transport and TCR-MHC signaling were also downregulated (Fig 3C). Here, HLA-C is linked to HIV-1 infection.