Master regulator expression and gene expression distributions in CD4
subtypes. (A) Read distributions along the master regulator Tbx21, Gata3, Rorc (RORγt), and Foxp3 loci in all cell types. The values are normalized to millions of total reads within each library. (B) Expression levels of master regulator transcription factors in all cell types. (C) Heatmap showing relative expression levels of the transcription factor loci in each biological replicate. Expression levels for each gene are scaled relative to the sample with the highest expression of that gene. (D) Kernel density estimates of expression level distributions for all cell types. Genes with zero counts were excluded from the distributions. Each of the samples displays the characteristic low expression (LE)/high expression (HE) shape with a shoulder of lowly expressed genes and a peak of highly expressed. (E) Expectation maximisation curve fitting of a Gaussian mixture model for the Th1 expression level kernel density estimate. Kernel density estimate is plotted in black whilst fitted Gaussian distributions are in yellow and purple. Boundaries between LE, Intermediate (Int) and HE expression were calculated using an FDR of 0.01 as previously described .