Figure 3. Cell Painting captures a more diverse sample space than L1000. (a) Uniform manifold approximation (UMAP) coordinates of all common perturbations (level 4 replicates) across all doses by Cell Painting (left) and L1000 readouts (right). We highlight select MOAs that are consistently different from DMSO controls. (b) Calculating goodness-of-fit metrics on k-means clustering solutions of level 4 replicate profiles for k = 2 to k = 40. We only considered compounds that passed the percent replicating 95% null threshold. We used 812 Cell Painting features and 978 L1000 features in each clustering iteration (see methods for more details) (c) Heatmaps of pairwise Spearman correlations of matched perturbations with the highest dose (10 uM) plus proteasome inhibitors at 20 uM and DMSO controls.
(High resolution image available in #23 )