Fig. 3: Identifying interferon-β stimulation signals across lymphoid and myeloid cells in a PBMC dataset.

We used sciRED to analyze PBMC scRNA-seq from eight lupus patients before and after an interferon-β (IFN-β) treatment. A FCA heatmap displaying covariate levels as rows and associated factors as columns. Arrows highlight factors F9 and F2, which capture stimulation signals. B Sorted factors based on FCA score values for the stimulated covariate level. F9 and F2 are the top factors associated with the stimulation covariate. C FIS heatmap illustrating the interpretability scores of the selected factors. Red boxes highlight factors capturing IFN-β stimulation. D Cell distribution over factors F9 and F2, colored based on cell type covariates. The red dashed line represents the diagonal line passing through the origin. Solid lines are the regression lines that fit each cell type. Lines with larger slopes than the diagonal represent cell types with higher association with F9, while lines with smaller slopes represent cell types more associated with F2. E Distribution of cells over factors F9 and F1 colored based on stimulation/control covariates, revealing distinct clustering between control and stimulated groups along the F9 axis. F Pathway analysis based on the top-loaded genes of factor F9. G Top 30 positively loaded genes of factor F9. H Distribution of cells over factors F1 and F2 colored by simulation state covariate (“stimulated” or “control”/non-stimulated). I Pathway analyses based on the top-loaded genes of factor F2. J Top 30 positively loaded genes of factor F2.