Fig. 1: Genome-wide screens performed on 3D cultures improve detection of cancer genes and pathways compared with those performed in 2D. | Nature

Fig. 1: Genome-wide screens performed on 3D cultures improve detection of cancer genes and pathways compared with those performed in 2D.

From: CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities

Fig. 1

a, Percentage of positive hits among the top 1,000 hits in the DepMap dataset10. Each point represents one cell line. b, Median CERES10 effects of oncogenes and tumour-suppressor genes (TSGs) (annotated in COSMIC30) among top 1,000 hits of 517 DepMap cell lines; each data point represents one cell line. c, Schematic for CRISPR screens in H23 cells. d, Distributions of phenotypes. Values on the x axis show the effect size of each gene and the y axis shows absolute phenotype score (T-score) (see Methods). Dot size represents absolute T-score. e, Phenotype scores for oncogenes and TSGs in top 1,000 hits in each condition. P values calculated using two-sided t-test. f, Enriched pathways among the top 1,000 hits from each condition analysed using PANTHER overrepresentation test (see Methods). Significance of enriched pathways were measured with Fisher’s exact test and the Benjamini–Hochberg false-discovery rates (FDR) were subsequently computed (x axis). The number of genes in enriched pathways is shown on the right. In all box plots, box limits mark upper and lower quartiles, whiskers represent 1.5× the interquartile range and points show outliers.

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