DOI: 10.6084/m9.figshare.13265159
title: Improving gene function predictions using independent transcriptional components - Raw Figure Data

description: Refer to the below descriptions of the files, also available in README.txt;<br><br>&gt;*****_medians_filegene_set_name : Name of gene setsize : Number of genes with prediction scores in that gene set gene_set_db : Name of host gene set collectionMethod : Method used to calculate prediction scores Subset : Median was calculated using member genes (n = size) or genes that are never members in that gene set collection. median_prediction_score: median prediction score (for gene sets with less than 10 or more than 500 genes = NA)<br>&gt;******_multifunctonality_filegene_set_name : Name of gene setmultifunctionality_score_correlation : Distance correlation between member prediction scores and multifucntionality score calculated using host gene set collection (Empty value = gene set size was outside 10-&gt;500 range)gene_set_db : Name of host gene set collectionmethod : Method used to calculate prediction scores<br>&gt;*****_old_version_comparison_filegene_set_name : Name of gene setsize : Number of genes that were added between v3.0 and v6.2gene_set_db : Name of host gene set collectiontype : version of gene set used to calculate prediction scores of these genesmethod : Method used to calculate prediction scoresMedian prediction score : median prediction score of subset of genes added in between v3.0 and v6.2<br>&gt;unbiased_clusteringFile with probe entrez_id to cluster mappingGROUP : cluster numberLABEL : Affymetrix probeENTREZID : Corresponding entrez numberSYMBOL : Corresponding symboluncharacterized : 0 or 1 if its an orf or LOC gene<br>&gt;cluster_predictabilityFile with cluster metrics GROUP : cluster numbersize : size of clustermedian_max_prediction : Maximum prediction score for each gene across 16 collections, cluster median.density : density metricmedian_multifunctionality : Median disctance correlation association to multifunctionality calculated using all genesets from all collectionsORF or LOC : amount of orf or LOC genes in cluster<br>&gt;durocher_comparison_figure_dataComparison data for Olivieri et al hit genesentrez_id : entrez numbervariable : Comparison is GO_DNA_REPAIR to GO_DNA_REPAIRpca_prediction_scores : PCA based prediction scorei.variable : Comparison is GO_DNA_REPAIR to GO_DNA_REPAIRica_prediction_scores : ICA based prediction scoreknown_link_to_DDR : 0 or 1 if it was called as known link in Olivieri et al<br>&gt;57_lps_network_all_genesICA-TC based prediction scores for Immunological Signatures gene set collection, of the subset of genes identified in a CRISPR-Cas9 screen that have a high co-functionality.entrez_number: Entrez ID of genegene_name: HGNC Gene Symbolgene_set: Immunological Signatures gene setvalue: Z-score of gene for gene set<br>&gt;HALLMARK_ICA_ZTpvalues_CORFsandLOCS_wardClusteredMatrix containing ICA-TC based prediction scores for all Corf and LOC genes, hierarchically clustered using ward's method and 1-cor(dist) as distance function.Columns correspond to hallmark gene sets, rows to genes.<br>&gt;HALLMARK_ICA_ZTpvalues_CORFsandLOCS_wardClustered_cutoff_0.8Cluster membership of the 835 Corf and LOC genes at a dendrogram cutoff height of 0.8GROUP: Cluster numberLABEL: HGNC Gene Symbol<br>&gt;HALLMARK_ICAvPCA_ZTpvalues_CORFsandLOCSComparison between ICA-TC based and PCA-TC based prediction scores of Hallmark gene sets for all Corf and LOC genes.gene: HGNC Gene Symbolvariable: gene seti.value: ICA-TC based prediction scorevalue: ICA-TC based prediction scorecategory: logical; 1 if i.value&gt;value, 0 if value&gt;i.value<br>&gt;ICAvPCA_GO_negviralregulation.txtComparison between ICA-TC based and PCA-TC based prediction scores of Hallmark gene sets for all Corf and LOC genes.entrez_id: Entrez ID of genevariable: gene seti.value: ICA-TC based prediction scorevalue: ICA-TC based prediction scoreknown_link: one of three strings: "yes" if gene is a member of the gene set; "no" if gene is not a member of the gene set, "screen" if the gene is one of the hits of the investigated CRISPR-cas screen<br>&gt;ICAvPCA_KEGG_LysosomeComparison between ICA-TC based and PCA-TC based prediction scores of Hallmark gene sets for all Corf and LOC genes.entrez_id: Entrez ID of genevariable: gene seti.value: ICA-TC based prediction scorevalue: ICA-TC based prediction scoreknown_link: one of three strings: "yes" if gene is a member of the gene set; "no" if gene is not a member of the gene set, "screen" if the gene is one of the hits of the investigated CRISPR-cas screen<br>&gt;Mouse_v_Human_barcode_spearman_correlations.txtSpearman correlations of mouse gene barcodes with ortholog human gene barcodes for each of the 16 gene set collections.mouse_gene: Mouse Entrez IDassoc_human: Entrez ID of corresponding human orthologspearman_r: Spearman correlation coefficientcollection: number corresponding to gene set collectionname: gene set collection name