DOI: 10.6084/m9.figshare.16746040
title: Data Files - Discovery of putative tumor suppressors from CRISPR screens reveals rewired lipid metabolism in acute myeloid leukemia cells

description: Files contained in here come from data files used and are related to analysis and figure generation. Code notebooks within the code folder will point to these specific data files. Not all data files used are uploaded to this specific repository to avoid redistribution of other published work (specifically HumanNet files, CCLE/DepMap CERES, clinical files - TCGA/OHSU/TARGET data, and the Cancer Gene Census from COSMIC).<br><br>Descriptions of data files contained in folder:<br>AML_age.txt - curated AML cell line data and age of derived patient.<br><br>Avana_Corrected_FC_2020_Q4.txt - Crispr cleanR corrected fold-change data of the 2020q4 Avana release.<br><br>Avana_NORM_MIXEM_FC_2020_Q4.txt - mu and sigma calculations Mixed model (k=2) for each screen's null distribution from Avana 2020q4.<br><br>avana_output_update_2020_Q4 - Primary data file used to complete figure analysis. Data file contains, depmap cell line id, entrez id, gene name, mean log2FC, CCLE expression, binary classification of mutation status, mixed z-score of gene, binary classification of cosmic TSG status, binary classification of non essential gene status, mean log2FC ranking, and hit_mix which represents PSG classification for each gene-cell line pair from of the Avana 2020q4 distribution.<br><br>bf_avana_2020q4_CRISPRcleanR_corrected.noNA - Crispr cleanR corrected bagel scores for the Avana 2020q4 distribution.<br>data_not_redistributed.xlsx - description and sources of data not uploaded to figshare to avoid redistribution of other published data. <br>dPCC-AML-qualFilt-varFilt.txt - filtered dPCC correlations related to figure 3.<br>fisher_edges_mix_hits_tsg.txt - Text file of all PSG gene pairs, and fishers test pvalue, and total count of gene observations as a hit (count not used for analysis).<br><br>fisher_net_mix_Z_fdr_0.001.txt - FDR &lt; 0.001 filtered network of all PSG gene pairs, and fishers test pvalue, and total count of gene observations as a hit (count not used for analysis). Main network used for analyses.<br><br>genes-significant-dPCC-with-chp1-cluster-zSTD-filter.txt - Genes filtered and selected for dPCC heatmap analysis of figure 3e.<br><br>Human_net_cutoff_results_updated.txt - Human net comparisons and cutoffs used for supplemental figure 4b.<br><br>Hunet_comparison_update.Rdata - Human net comparisons and cutoffs used for supplemental figure 4a.<br>JACKS_result_gene_JACKS_results.txt - Crispr cleanR corrected JACKS scores for Avana 2020q4 distribution. <br>log_normalmixEM.txt - log file of mixture model iterations of avana2020q4.<br><br>matrix-GMMZ-qualFilter-varFilter-9055genes-659cells-17aml.txt - Selecting appropriate AML cells for dpcc analysis in figure 3e.<br>metabolite_error.txt - Metabolite variance measurements used in determining viable metabolites for analysis. Metabolites that had measurements below error were not used.<br><br>Mix_Z_pr_values_updated.txt - precision recall measurements and associated mixed z-scores of pr cutoffs. used to determine FDR cutoff measurements. <br><br>NEGv1.txt - Non essential genes from bagel.<br><br>PTEN_CN.txt - PTEN copy number values from CCLE.<br>Sanger_Corrected_FC.txt - Crispr cleanR corrected fold-change data of the Sanger 2019 release.