Extended Data Figure 5. DIALOGUE identifies mis-localized cells and disease MCPs in single-cell data.

(a) ROC curves showing the true positive (y axis) and false positive (x axis) rate when predicting mis-localized cells of each major subset (panels) with different types of “contamination” with cells that are either from the same layer (LP/EPI) within control (black, from replicate biopsy) or UC (blue; from adjacent biopsy with a different clinical status: inflamed or non-inflamed); or from a different layer but same clinical status, when considering either all samples (green) or only samples from control (yellow) or UC patients (red). (b) UC multicellular program genes. Average expression (Z score residuals after regressing out the associations with the LP/EPI location, red/blue color bar) of top genes (columns) from the UC multicellular program, sorted by their pertaining cell type (top color bar), across samples (rows), sorted by Overall Expression (right, Online Methods), and labeled by clinical status, location and patient ID (left color bar). (c) Melanoma MCP1. Average expression (Z score, red/blue color bar) of top genes (columns) from MCP1 identified in four different cell types (top color bar), across melanoma tumor samples (rows), sorted by Overall Expression of MCP1 (right, Online Methods), and labeled by treatment status and ICB response (left color bar).