DOI: 10.6084/m9.figshare.14963561
title: Webster Supplemental Output

description: # Webster Supplemental Output<br>This repository contains data to support Pan et al., "Sparse dictionary learning recovers pleiotropy from human cell fitness screens". There are four groups of data:<br><br>## Tables (xlsx)<br>These are the excel files to support manuscript submission. Each file contains a Readme as the first sheet with data descriptions.<br>* Table S1: Webster output from genotoxic fitness screen data: dictionary matrix, loadings matrix, and annotations.<br>* Table S2: UMAP embedding coordinates for genotoxic fitness screen data.<br>* Table S3: Webster output from Cancer Dependency Map data: dictionary matrix, loadings matrix, and annotations.<br>* Table S4: UMAP embedding coordinates for Cancer Dependency Map data.<br>* Table S5: Mass spectrometry peptide counts for immunoprecipitations. <br>* Table S6: The maximum subcellular localization score for each of the functions learned from Cancer Dependency Map data.<br>* Table S7: Compound-to-function loadings for annotated compounds from PRISM primary and secondary screens.<br><br><br>## depmap (tsv)<br>These are flat files that are the basis for the Tables above, and represent the raw input and outputs of Webster.<br>* depmap_cell_line_info<br>Annotations for each cell line. <br>* depmap_dictionary<br>Webster dictionary matrix inferred from fitness data.<br>* depmap_fn_annot_gprofiler<br>Annotations derived from gProfiler using gene loadings on each function.<br>* depmap_fn_biomarkers<br>Random forest modeling results using cell line features to predict the fitness effect of ecah function in the dictionary.<br>* depmap_fn_manual_name<br>Manual name for each function, derived from above resources.<br>* depmap_fn_subcell_raw_matrix<br>Matrix cross product between Go et al. localization scores, and our gene-to-function loadings. <br>* depmap_fn_subcell<br>The subcell localization information used for coloring functions in the global embedding.<br>* depmap_gene_loadings<br>Webster gene-to-function loadings matrix, inferred from fitness data.<br>* depmap_gene_meta<br>Gene-centric information and useful links.<br>* depmap_input<br>Pre-processed Cancer Dependency Map (DepMap) data that is the input to Webster.<br>* depmap_umap<br>Embedding coordinates.<br><br><br>## genotoxic (tsv)<br>Same structure as above, but for Webster input from the smaller genotoxic fitness dataset (Olivieri et al 2020)<br>* genotoxic_dictionary<br>* genotoxic_gene_loadings<br>* genotoxic_gene_meta<br>* genotoxic_input<br>* genotoxic_umap<br><br>## prism (tsv)<br>Results of projecting PRISM screening data (Corsello et al 2020) into a latent space inferred from Depmap data.<br>* prism_embedding<br>Same as depmap_umap above, except with the addition of selected compounds into the embedding, as well sa compound meta information useful for labeling the plot.<br>* prism_primary_imputed<br>Input for projection into the Webster latent space. This is preprocessed and filtered for high-variance, well annotated compounds. <br>* prism_primary_meta <br>Compound annotations for primary screen data. <br>* prism_primary_omp<br>Compound-to-function loadings learned by Orthogonal Matching Pursuit.<br>* prism_primary_proj_results<br>Summary statistics for projection results.<br>* prism_secondary_imputed<br>Input for projection into the Webster latent space. This is preprocessed and filtered for high-variance, well annotated compounds, treated at many doses.<br>* prism_secondary_meta<br>Compound annotations for secondary screen data. <br>* prism_secondary_omp<br>Compound-to-function loadings learned by Orthogonal Matching Pursuit.<br>* prism_secondary_proj_results<br>Summary statistics for projection results.<br><br><br>