Fig. 3 | Nature Communications

Fig. 3

From: Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance

Fig. 3

Predicting E. coli essential genes from CRISPRi screening. a Volcano plot of gene fitness and −Log10P value of two-tailed MWU test. Dashed lines represent a threshold (FDR = 0.05) for calling hits based on the screening score (see Methods). Four groups of genes are shown: blue, 313 essential genes from the Keio collection (Supplementary Data 11); gray, non-essential genes from the Keio collection and assigned as true negatives by CRISPRi screening; purple, false-positive “required” genes assigned by CRISPRi screening, potentially because of downstream Keio collection essential genes in operons transcribed as polycistronic mRNA; green, other genes found by CRISPRi screening to significantly inhibit cell growth. b and c ROC curves indicate the performances of different methods in identifying essential genes when considering all 4140 protein-coding genes (b) and 702 protein-coding genes with smaller coding regions (<400 bp) (c). True-positive rates and false-positive rates were calculated using the gold-standard set of essential and nonessential genes from the Keio collection1. Shown are ROC curves for CRISPRi screening (55,671 sgRNAs) (red, CRISPRi score), a benchmark Tn-seq experiment (152,018 unique transposon insertions) (yellow, Wetmore et al.25), a recently reported Tn-seq dataset with unprecedented-density transposon library size (901,383 members) (purple, Goodall et al.29) and a widely used transposon insertion—based genetic footprinting dataset (blue, Gerdes et al.28). The dashed line represents a random guess of the essential genes

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