Differences between inbuilt and custom signature genes, and debCAM cell-type specific genes.

(A) Expression of inbuilt signature genes (N=547) in 22 leukocyte subsets, curated by the CIBERSORTx team from microarray gene expression. For each gene (row), expression is centred to the mean and scaled by the standard deviation across cell types (column). Columns are split by the collapsed classes. CD4: T cells CD4 naive, T cells CD4 memory resting, T cells CD4 memory activated, T cells follicular helper, and T cells regulatory (Tregs); CD8: T cells CD8; CD14: Monocytes, Macrophages M0, Macrophages M1, and Macrophages M2; CD19: B cells naive and B cells memory; PCs: Plasma cells; GammaT: T cells gamma delta; NK: NK cells resting and NK cells activated; Dendritic: Dendritic cells resting and Dendritic cells activated; Mast: Mast cells resting and Mast cells activated; Eos: EosinophilsPMN: Neutrophils (B) Expression of custom signature genes (N=1589), derived from our sorted-cell RNAseq expression in 80 training subjects using CIBERSORTx. Expression is centred and scaled across cell types (column) by gene (row). (C) Numbers (No.) of debCAM cell-type specific genes by cell type (row) and selection criteria (column). debCAM, which does not have the signature matrix, selects the cell-type-specific genes, that are over-expressed in one cell type versus everyone (OVE). OVE fold change (FC) of 1, 2, 5 and 10 were used in our sorted cell expression of 80 training subjects. The first four principal components from PCA analysis of (D) inbuilt, (E) custom signature and (F) debCAM cell type specific gene expression in test samples. Each dot is a sample, coloured by cell type and shaped by sequencing batch. (PDF)