Webster Supplemental Output

# Webster Supplemental OutputThis 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_infoAnnotations for each cell line. * depmap_dictionaryWebster dictionary matrix inferred from fitness data.* depmap_fn_annot_gprofilerAnnotations derived from gProfiler using gene loadings on each function.* depmap_fn_biomarkersRandom forest modeling results using cell line features to predict the fitness effect of ecah function in the dictionary.* depmap_fn_manual_nameManual name for each function, derived from above resources.* depmap_fn_subcell_raw_matrixMatrix cross product between Go et al. localization scores, and our gene-to-function loadings. * depmap_fn_subcellThe subcell localization information used for coloring functions in the global embedding.* depmap_gene_loadingsWebster gene-to-function loadings matrix, inferred from fitness data.* depmap_gene_metaGene-centric information and useful links.* depmap_inputPre-processed Cancer Dependency Map (DepMap) data that is the input to Webster.* depmap_umapEmbedding 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_embeddingSame 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_imputedInput 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_ompCompound-to-function loadings learned by Orthogonal Matching Pursuit.* prism_primary_proj_resultsSummary statistics for projection results.* prism_secondary_imputedInput for projection into the Webster latent space. This is preprocessed and filtered for high-variance, well annotated compounds, treated at many doses.* prism_secondary_metaCompound annotations for secondary screen data. * prism_secondary_ompCompound-to-function loadings learned by Orthogonal Matching Pursuit.* prism_secondary_proj_resultsSummary statistics for projection results.