Webster Supplemental Output

Name: Webster Supplemental Output
Creator: Pan, Joshua
Published: 2022-01-19 00:00:00
License: 暂无描述

Figshare2022-01-19 更新2026-04-08 收录

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

提供机构：

Pan, Joshua

创建时间：

2022-01-19

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