Fig. 3

scMAGeCK on other phenotypes. a The apoptosis selection score of different genes in MCF10A CROP-seq datasets treated with doxorubicin (y-axis) and with mock control (x-axis). Genes with FDR < 0.1 are highlighted in red. Here the average expression of signature genes in an apoptosis gene set in MSigDB is served as a marker. The signature comes from genes that are downregulated in a breast cancer cell line (ME-A) undergoing apoptosis in response to doxorubicin (ID: GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN). b The target-marker-phenotype network in T cell CROP-seq dataset. Target genes are genes that are screened in CROP-seq dataset, while markers that are known to be associated with resting T cells, activating T cells, and proliferation are selected. Gene regulatory relationship from non-stimulating and stimulated cells is shown in dashed and solid lines, respectively. Genes are selected based on the FDR cutoff 0.1 from scMAGeCK-RRA