Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data
Fig 8
Evaluating IGNITE predictions of gene knockouts in hPSC differentiation.
A. Difference in cluster composition between WT- and KO-generated data, averaged across 150 replicates. Rows correspond to simulated single-gene KOs, columns to clusters (1–5) or excluded cells. Rows were ordered by hierarchical clustering, which also identified 11 groups shown by colour. Red indicates an increase after KO, blue a decrease. B. PCA of cluster composition across conditions: WT input, WT-generated, and each single-gene KO. Each point corresponds to one condition and is positioned by the fractions of cells across clusters (1–5) and excluded cells (fractions for generated conditions are averaged over 150 replicates). Colours indicate the groups defined in Fig 8A. KO conditions corresponding to the genes shown in A are indicated. C. Differentiation score for selected KO genes, chosen to overlap with those analysed in [31], computed as described in Methods. The axis break highlights the outlier magnitude of POU5F1.