IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data
Fig 4
Testing the known effect of eight gene perturbations on in silico developmental trajectories.
(A) Schematic of performed gene perturbations. In OE, the gene is always expressed (represented with 1) and in KO the gene is always silent (represented with 0). (B) PCA plot of the simulated developmental trajectories under perturbed conditions are overlaid on the binarized scRNA-seq. The perturbations include KO of Notch1, KO of Tcf7, KO of Bcl11b, KO of Runx1, KO of Tcf12, KO of Myb, OE of Tcf12 and the double perturbation, OE of Tcf7 and KO of Notch1 at the same time. (C) Expression states of the model attractors under perturbations. Genes that are expressed (1) and not expressed (0) are represented with blue and grey squares, respectively. (D) Percentage of similarity between the model attractors under perturbations (vertical axis) and the binarized expressions of CLP, ETP, DN2A, DN2B, and DN3A cells (horizontal axis) [38] (left). Description of known effect of the gene perturbation on T-cell development (right).