Extended Data Fig. 5: Th-associated genes are not the main drivers of Teff heterogeneity.
From: Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes
a, Distribution of Top 6 PCs of Teffs from all hash-tagged samples, with cell cycle genes regressed out. Genes that are Th-associated are highlighted. b, Co‐expression of key cytokines across all samples. Mean Pearson gene:gene correlation of cytokine genes across all samples. Only significantly correlated cytokines are colored (p < 0.05, χ² test). Significant P values: Il4/Il13 6.3 × 10−3, Il4/Il5 1.8 × 10−98, Il5/Il13 5.5 × 10−129, Il17a/Il17f 1.3 × 10−4. c, Coregulated gene modules in Teff single-cells. Gene:gene correlation between 588 most variable genes was calculated independently within each condition/infection of the single-cell datasets, then averaged between conditions. 16 gene modules were determined by Affinity Propagation within this matrix, annotated at right. d, Overlay of average expression of these gene modules on Teff tSNE (per 2c) with barplots showing genes with highest mean correlation (full list in Supplementary Table 3).
