Fig. 2

Associations with the expression of Ki-67 (MKI67), a proliferation marker. a, b The rankings of genes that are positively (a) or negatively selected (b) on MKI67 expression. Here, positive selection in a indicates single cells with certain target gene knockout (black rectangle on the top) have higher MKI67 expression. c The MKI67 selection score in stimulating and non-stimulating T cells in the T cell CROP-seq dataset. Genes performed in two different patient samples (D1/D2) are marked with different colors, and genes with FDR < 0.1 are highlighted. The selection score is calculated based on the p values reported from RRA, with direction depending on whether it is a positively (or negatively) selected genes. See “Methods” for more details. d, e The ranking of selected genes in c in genome-wide CRISPR screening, including negative selection ranking (d) and positive selection ranking (e). f The MKI67 selection score and p values calculated from scMAGeCK-LR in K562 dataset. Essential genes (ribosomal subunits and proteasomes) are marked in blue, while the tumor-suppressor-like enhancer of interest (chr12:102249040-102249063) is highlighted in red. Inset: the distribution of MKI67 selection score between essential genes and other genes. p value is calculated using Wilcox rank sum test. g The chromosome view of the enhancer chr12:102249040-102249063. h, i The DRAM1 and GNPTAB selection score and their corresponding p values. The enhancer chr12:102249040-102249063 is highlighted in red