These upregulated genes were also core signature genes used to identify Tr1 cells within the sub-clustered CD4 T cells at day 0 and 28 (Fig. 5a/b, Supplementary Data 7), suggesting that while the overall frequency of Tr1 cells in the periphery didn’t change with infection (Supplementary Fig. 13), the regulatory capacity of Tr1 cells was increased during malaria. Here, CD4 is linked to infection.