Fig. 2
Characterization of transcriptional single-cell response groups. a Left: Schematic of signature database. The expression of a bulk sample of simulated DCs (Si) is compared to the expression of a mock control (Mi). Highly ranked upregulated and downregulated genes comprise the signature \( {\upsigma}_{\mathrm{i}} \). Middle: \( {\upsigma}_{\mathrm{i}} \) is applied to all cells in the study and FastProject identifies pairs of expression data projections and \( {\upsigma}_{\mathrm{i}} \) for which \( {\upsigma}_{\mathrm{i}} \) varies coherently across the projection. Right: Coherent \( {\upsigma}_{\mathrm{i}} \) values are binned by cluster to nominate specific cluster contrasts as biologically meaningful. b Cumulative distribution function (CDF) comparisons for single cells from each cluster identified in Additional file 1: Figure S1 with FastProject gene signatures derived from GSE14000 [57], GSE22589 [29], GSE18791 [58], and GSE2706 [59] (see “Methods”). The single-cell signature value quantifies the extent to which each cell is polarized toward a stimulated instead of unstimulated expression state. Clusters with gene expression signatures more closely mapping to the stimulated condition shift right, while clusters characteristic of unstimulated shift left. Kolmogorov–Smirnov (KS) tests show significant differences in these signatures between the first three clusters (c1, n = 220; c2, n = 26; c3, n = 35). c Potential genes specific for c1 (cyan), c2 (orange), shared between c1 and c2 (white) or inconsistent across individuals (gray). Individual volcano plots of negative log IDR vs mean differential log-expression between clusters c1 and c3–5 (right) and c2 vs c3–5 (left; see “Methods”). d Selected ingenuity pathway analysis (IPA) (see “Methods”) results for canonical pathways (Benjamini–Hochberg q value < 0.01) and upstream regulators (Bonferroni p value < 0.05) significantly deactivated (blue), neutral (white: with z score; black: without z score), or activated (orange) in c1 vs c3–5. e Comparison of putative upstream regulators from IPA for c1 vs c2–5 and c2 vs c3–5 (see “Methods”)