Figure 3.

Subject variability in immune and disease-relevant genes and pathways. (a) Magnitude (log₂ F statistic) of the variability in expression of genes between different cell types (x) and between subjects (y). 1284/7034 (18.3%) of genes are above the subject specificity significance line (FDR < 0.05, multiple comparison correction) and are classified as subject-specific. Several MHC class II genes (HLA-X) are strongly subject-specific, consistent with previous findings³⁵. (b) KEGG pathways grouped into categories and their enrichment (Z-score from 2-proportion Z-test) among the top 250 diurnally and subject-varying genes vs all genes. Immune system and disease pathways are significantly enriched (p = 0.029), supportive of the conclusion that immune and disease-related genes are highly subject dependent. The large circles indicate the enrichment of the category overall, and the sizes of the smaller pathway points indicate the number of genes associated with the pathway. (c) Subject and cell type specific gene examples for each subject and cell type with the upper row displaying the trace of mean gene expression across time-points and the bottom row showing gene abundance shifts for the subjects of interest.