Figure 7. Normalisr revealed gene-level cellular pathways and functional modules in the single-cell co-expression network.

a, b Single-cell co-expression was dominated by house-keeping programs (a), whose iterative removal recovered cell-type-specific programs (b), according to the top 4 GO enrichments (Y) of the top 100 principal genes in the co-expression network. P values and odds ratios are shown in cyan (top X) and blue (bottom X). c Single-cell transcriptome-wide co-expression network (major component) after house-keeping program removal highlighted functional gene sets for dysfunctional T cells. Edge color indicates positive (red) or negative (blue) co-expression in Pearson R. Node color indicates DE logFC between dysfunctional and naive T cells. Node size indicates average expression level in dysfunctional T cells. Node border annotates known gene functions. Dashed circles indicate major gene co-expression clusters. d Single-cell co-expression recovered cell-type-specific and generic gene functional similarities, according to significant over-abundances of edges between genes in the same GO or KEGG pathway, as highlighted in red.