Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data
Fig 7
Inference and validation of IGNITE in hPSCs: GRN and generated data.
A. Pearson correlation matrix of gene activity in the input dataset (human PSCs differentiation scRNA-seq data with LogNorm, PST, and MB). B. Pearson Correlation matrix of the gene activity generated with IGNITE. C. PCA of gene activity for three datasets: input, from scRNA-seq data with LogNorm, PST, and MB (left), IGNITE-generated wild type (middle), and IGNITE-generated knockout of POU5F1 (right). The colour gradient represents the cell density within each square area. Dashed contours denote cluster boundaries defined on the input (left) and reused for the generated datasets. D. Fraction of cells assigned to clusters (1–5) or excluded areas, for the same three datasets shown in C. For generated data, bars show means across replicated simulations (150 simulated datasets; error bars indicate SEM). Bar colours match the clusters in C.