The computational models were based on the overall transcript levels of a number of cytokines (IL-18, IL-12, IFN-γ, IL-21, IL-6, IL-17, IL-23, IL-4, TGF-β, IL-2, IL-10), receptors (IL-18r, IL-12r, IFN-γr, Il-6r, IL-17r, IL-23r, IL-4r, TGF-βr, IL-2r, IL-10r), and a subset of transcription factors (Tb21, Gata3, Foxp3, Rorc) from our RNA-Seq study to determine the likelihood for each CD4+ subset and overall CD4+ subset composition throughout the course of infection (Fig. 4, Supplementary Figure S6). Here, IFNG is linked to infection.