Extended Data Fig. 4: Characterization of ADaM pan-cancer core fitness genes.
From: Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens
a, The 553 pan-cancer core fitness genes in reference essential gene sets are shown9,10. Respective recall and enrichment significance P values from a hypergeometric test when considering the whole set of genes targeted in the CRISPR–Cas9 screen as the background population (n = 17,995). The 132 newly identified core fitness genes fall outside of these reference gene sets. b, c, Pathways (b) and gene families (c) enriched in the 132 newly identified pan-cancer core fitness genes (Benjamini–Hochberg-adjusted hypergeometric test P < 0.05). d, Comparison of the ADaM core fitness genes with two previously reported reference sets9,10 of essential genes in terms of number of genes, estimated precision and recall (the genes included in reference gene sets corresponding to cellular essential process were considered to be true-positive genes). e, FDRs of putative context-specific fitness genes at different thresholds of reliability (n = 7,393, 2,233, 426 and 82 putative context-specific fitness genes, respectively, for thresholds equal to 20, 50, 100 and 200 of log-likelihood of skewed t-distributions). f, Clustering of cancer types based on core fitness gene similarity (left) and numbers of cancer-type core-specific fitness genes exclusive to each cancer type (right). g, Basal expression of cancer-type specific core fitness genes (n, across tissues indicated in Fig. 1c) in matched normal tissues compared with all the other genes in the genome, across cancer types (as indicated by the different colours). Five genes were identified as core fitness genes in a single cancer type and are not expressed at the basal level (<5% quantile) in matched normal tissue (red points). Cancer types are coloured as shown in f. Box-and-whisker plots show interquartile ranges and 95th percentiles, with sample sizes indicated in f (right), centres indicate median values.
