Genome-wide association analysis identifies genetic correlates of immune infiltrates in solid tumors
A: CD4 is co-expressed with both T cell (CD3E) and myeloid linege (CSF1R) markers in melanoma. Scatter plots of CD4, CD3E, and CSF1R transcript levels from a single-cell RNA-seq data study of melanoma patients (Tirosh et al.). Only CD45 positive cells (PTPRC, expression > 1) are shown. Gaussian noise (s.d. = 0.25) was added to the transcript estimates to improve data visualization (log2 scale). B: Mutual rank-based co-regulatory network around FOXP3 in TCGA. All solid tumor samples in the TCGA pan-cancer data release were used to create the mutual rank correlation network. Color saturation and thickness of lines represent strength of correlation. CCR8 and FOXP3 were selected to create a regulatory T cell (Treg) signature for estimating Treg content in tumors. C: Mutual rank-based co-regulatory network around FOXP3 in Tirosh et al. single cell melanoma RNA-seq data. D: Mutual rank-based co-regulatory network around macrophage marker VSIG4 in TCGA. VSIG4, CD163, and MS4A4A were selected to create a signature to estimate macrophage content in tumors.