Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data
Fig 4
GRN inferred by IGNITE and comparison with literature-supported interactions.
A. Interaction matrix of the GRN inferred with IGNITE from the input dataset (log-normalized scRNA-seq with PST and MB). Genes are grouped as in Fig 1C: naïve (blue), formative early (yellow), formative late (red), and others (grey). Matrix elements (i,j) represent the interaction from regulator j to target i, with positive (red) and negative (blue) values. B. Subnetwork of 18 interactions reported in the literature. Only the involved genes are shown, coloured as in A. Arrows denote activating (red) or inhibitory (blue) interactions. C. Subnetwork of literature-reported interactions correctly recovered by IGNITE. The arrows represent the interactions that IGNITE inferred with the correct sign.