Fig. 2: Evaluation of SCORPION’s ability to detect changes in transcription factor activity and their impact on target genes.

a, Differences in the distribution of the edge weights for the Hnf4α transcription factor in Hnf4αγ^WT and Hnf4αγ^DKO mouse intestinal epithelium cells. b, Distribution of the paired weight differences between the edges of the Hnf4α transcription factor (\(\hat{\mu }\) and P were calculated using a one-sample two-sided t-test). c, Spearman correlation (\(\hat{\rho }\)) of the edge weights for the Hnf4α transcription factor in Hnf4αγ^WT and Hnf4αγ^DKO mouse intestinal epithelium cells. Genes outside the 95% confidence interval are color-coded and labeled (in red if upregulated and in blue if downregulated). d, GSEA of enterocyte marker genes using the paired differences between the edge weights of the Hnf4α transcription factor (NES and P_adj were computed using the GSEA test). e, Differences in the distribution of the edge weights for the Hnf4γ transcription factor in Hnf4αγ^WT and Hnf4αγ^DKO mouse intestinal epithelium cells. f, Distribution of the paired weight differences between the edges of the Hnf4γ transcription factor (\(\hat{\mu }\) and P were calculated using a one-sample two-sided t-test). g, Spearman correlation (\(\hat{\rho }\)) of the edge weights for the Hnf4γ transcription factor in Hnf4αγ^WT and Hnf4αγ^DKO mouse intestinal epithelium cells. Genes outside the 95% confidence interval are color-coded and labeled (in red if upregulated and in blue if downregulated). h, GSEA of the enterocyte marker genes using the paired differences between the edge weights of the Hnf4γ transcription factor (NES and P_adj were computed using the GSEA test). i, UMAP of human ESCs. 8-cell-like cells are highlighted. j, Differences in the distribution of the edge weights for the DUX4 transcription factor in DUX4^WT and DUX4^OE human ESCs. k, Distribution of the paired weight differences between the edges of the DUX4 transcription factor (\(\hat{\mu }\) and P were calculated using a one-sample two-sided t-test). l, Spearman correlation (\(\hat{\rho }\)) of the edge weights for the DUX4 transcription factor in DUX4^WT and DUX4^OE human ESCs. Genes outside the 95% confidence interval are color-coded and labeled (in red if upregulated and in blue if downregulated). m, GSEA of the 8-C-like cell marker genes using the paired differences between the edge weights of the DUX4 transcription factor (NES and P_adj were computed using the GSEA test).

Source data