A question came up recently about how the gene expression patterns influenced position in UMAP space.
For many CRISPRi perturbations, we observe that grit really nicely tracks titration. For example, in HSPA5 we observe that with increasing relative activity (facets of the plot), we observe an increase in single cell grit.
We are interested in how the measured expression of HSPA5 behaves in this space.
For HSPA5, there does not appear to be a relationship.
(Note the UMAP coordinates are different from the last results - I reran UMAP after reprocessing in #9)
This lack of relationship is not universal. For example, here are the plots for HSPE1
A question came up recently about how the gene expression patterns influenced position in UMAP space.
For many CRISPRi perturbations, we observe that grit really nicely tracks titration. For example, in HSPA5 we observe that with increasing relative activity (facets of the plot), we observe an increase in single cell grit.
We are interested in how the measured expression of HSPA5 behaves in this space.
For HSPA5, there does not appear to be a relationship.
(Note the UMAP coordinates are different from the last results - I reran UMAP after reprocessing in #9)
This lack of relationship is not universal. For example, here are the plots for HSPE1
See https://github.com/broadinstitute/grit-benchmark/blob/main/2.compare-metrics/perturb-seq/0.compare-activity-score.ipynb for all UMAP figures
cc @avtar00