Additional file 2: of Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

Figure S1. CRISPR-KO screening data quality assessment. (A) Average correlation between sgRNAs read-count replicates across cell lines. (B) Receiver operating characteristic (ROC) curve obtained from classifying fitness essential (FE) and non-essential genes based on the average logFC of their targeting sgRNAs. An example cell line OVCAR-8 is shown. (C) Area under the ROC (AUROC) curve obtained for cell lines from classifying FE and non-essential genes based on the average logFC of their targeting sgRNAs. (D) Recall for sets of a priori known essential genes from MSigDB and from literature when classifying FE and non-essential genes across cell lines (5% FDR). Each circle represents a cell line and coloured by tissue type. Box and whisker plots show median, inter-quartile ranges and 95% confidence intervals. (E) Genes ranked based on the average logFC of targeting sgRNAs for OVCAR-8 and enrichment of genes belonging to predefined sets of a priori known essential genes from MSigDB, at an FDR equal to 5% when classifying FE (second last column) and non-essential genes (last column). Blue numbers at the bottom indicate the classification true positive rate (recall). Figure S2. Assessment of copy number bias before and after CRISPRcleanR correction across cell lines. sgRNA logFC values before and after CRISPRcleanR for eight cell lines are shown classified based on copy number (amplified or deleted) and expression status. Copy number segments were identified using Genomics of Drug Sensitivity in Cancer (GDSC) and Cell Line Encyclopedia (CCLE) datasets. Box and whisker plots show median, inter-quartile ranges and 95% confidence intervals. Asterisks indicate significant associations between sgRNA LogFC values (Welchs t-test, p