Data repository: 'Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens'

Input data required to reproduce the results of the manuscript.

• Achilles_gene_effect.csv (Not provided with this upload)

  • Gene effect scores available publicly through the online  DepMap portal. Rows are samples, columns are genes.

  • Downloaded from the Broad Institute DepMap portal release version DepMap Public 20Q2 Primary Files - https://depmap.org/portal/download/all/ 

  • Direct link to download - https://ndownloader.figshare.com/files/22629068 

• 20Q2_GLS_fdr.npy

  • Output from GLS pipeline. 

• 20Q2_GLS_sign.npy

  • Output from GLS pipeline. 

• Depmap_q2_2020_nona_mean.tsv

  • Processed version of DepMap 20Q2 data (Achilles_gene_effect.csv). Rows are genes, columns are samples. Postfixes of gene names are discarded. In sample names, ‘-’ is replaced by ‘.’.  NA values are imputed with gene-wise average. 

• Depmap_q2_2020_nona_mean_rst_clp_mms.tsv

  • Processed version of Depmap_q2_2020_nona_mean.tsv. Rows are genes, columns are samples. Data is  row-standardized, clipped between -4 and 4, and min-max scaled to range between -1 to 1.

• All_genes_20q2.txt

  • List of gene names from DepMap 20Q2 data. 

• Mitochondial_genelist_1_26_2021_genes.tsv

  • List of genes associated with  mitochondrial protein complexes curated from mitocarta30 inventory of mammalian mitochondrial proteins and pathways

•  Olfactory_receptors.csv

  • List of olfactory receptor genes

• Ae_tanh_e1_depmap_20q2

  • Normalized DepMap 20Q2 data generated by Autoencoder pipeline for latent space sizes of 1,2,3,4,5, and 10 and epoch 1.

    •  20q2_epochs_1_latent_1_normalized_ae.tsv

    •  20q2_epochs_1_latent_2_normalized_ae.tsv

    •  20q2_epochs_1_latent_3_normalized_ae.tsv

    •  20q2_epochs_1_latent_4_normalized_ae.tsv

    •  20q2_epochs_1_latent_5_normalized_ae.tsv

    •  20q2_epochs_1_latent_10_normalized_ae.tsv

Outputs generated by normalization pipelines.

• ae - outputs from Autoencoder normalization pipeline

  • Un-normalized data

    • Complex_AUPRC_depmap_q2_2020_ae_0.txt

    • FLEX outputs - analysis results

      • CORUM_complex_Diversity_data_depmap_q2_2020_ae_0.tsv

      • CORUM_complex_Diversity_plot_depmap_q2_2020_ae_0.pdf

  • AE-normalized data

    • normalized_ae_xx.tsv (*xx=1,2,3,4,5,10)

    • FLEX outputs - analysis results

      • Complex_AUPRC_normalized_depmap_q2_2020_ae_xx.txt  (*xx=1,2,3,4,5,10)

      • CORUM_complex_Diversity_data_normalized_depmap_q2_2020_ae_xx.tsv  (*xx=1,2,3,4,5,10)

  • AE-reconstructed data

    • projected_ae_xx.tsv  (*xx=1,2,3,4,5,10)

    • FLEX outputs - analysis results

      • CORUM_complex_Diversity_data_projected_depmap_q2_2020_ae_xx.tsv (*xx=1,2,3,4,5,10)

  • FLEX PR plots

    • depmap_q2_2020_ae_CORUM_complex_PR_.pdf

    • depmap_q2_2020_ae_no_mitoCORUM_complex_PR_.pdf

• rpca - outputs from Robust Principal Component Analysis normalization pipeline

• (*Note - mapping of RPCA filename postfix with lambda hyperparameter value used in the figure legend: 0.7=.0049; 0.8=.0056; 0.9=.0063; 1=.007; 1.1=.0077; 1.2=.0084; 1.3=.0091)

  • Un-normalized data

  • FLEX outputs - analysis results

    • CORUM_complex_Diversity_data_depmap_q2_2020_rpca_0.tsv

    • CORUM_complex_Diversity_plot_depmap_q2_2020_rpca_0.pdf

    • Complex_AUPRC_depmap_q2_2020_rpca_0.txt

  • RPCA-normalized data

    • normalized_rpca_xx.tsv (*xx=0.7,0.8,0.9,1,1.1,1.2,1.3)

    • FLEX outputs - analysis results

      • Complex_AUPRC_normalized_depmap_q2_2020_rpca_xx.txt (*xx=0.7,0.8,0.9,1,1.1,1.2,1.3)

      • CORUM_complex_Diversity_data_normalized_depmap_q2_2020_rpca_xx.tsv (*xx=0.7,0.8,0.9,1,1.1,1.2,1.3)

  • RPCA-reconstructed data

    • projected_rpca_xx.tsv (*xx=0.7,0.8,0.9,1,1.1,1.2,1.3)

    • FLEX outputs - analysis results

      • CORUM_complex_Diversity_data_projected_depmap_q2_2020_rpca_xx.tsv (*xx=0.7,0.8,0.9,1,1.1,1.2,1.3)

  • FLEX PR plots

    • depmap_q2_2020_rpca_CORUM_complex_PR_.pdf

    • depmap_q2_2020_rpca_no_mitoCORUM_complex_PR_.pdf

• pca - outputs from Principal Component Analysis normalization pipeline

  • Un-normalized data

    • Complex_AUPRC_depmap_q2_2020_pca_0.txt

    • FLEX outputs - analysis results

      • CORUM_complex_Diversity_data_depmap_q2_2020_pca_0.tsv

      • CORUM_complex_Diversity_plot_depmap_q2_2020_pca_0.pdf

  • PCA-normalized data

    • normalized_pca_xx.tsv (*xx=1,3,5,7,9,11,13,15,17,19)

    • Complex_AUPRC_normalized_depmap_q2_2020_pca_xx.txt (*xx=1,3,5,7,9,11,13,15,17,19) 

    • CORUM_complex_Diversity_data_normalized_depmap_q2_2020_pca_xx.tsv (*xx=1,3,5,7,9,11,13,15,17,19) 

  • PCA-reconstructed data

    • projected_pca_xx.tsv (*xx=1,3,5,7,9,11,13,15,17,19)

    • CORUM_complex_Diversity_data_projected_depmap_q2_2020_pca_yy.tsv (*yy=5,7,9,11,13,15,17,19)

  • FLEX PR plots

    • depmap_q2_2020_pca_CORUM_complex_PR_.pdf

    • depmap_q2_2020_pca_no_mitoCORUM_complex_PR_.pdf

• onion - outputs from Onion normalization pipeline and benchmarking 

  • Normalized networks (ONION)

    • snf_run_pca_10_5_3.Rdata

    • snf_run_rpca_7_5_5.Rdata

    • snf_run_ae_7_5_5.Rdata

  • GLS normalized network

    • gls_20q2_inv_sign_FDR.Rdata

  • FLEX outputs - analysis results

    • AUPRC data

      • Complex_AUPRC_depmap_q2_2020_onion_0.txt

      • Complex_AUPRC_pco.txt

      • Complex_AUPRC_rpco.txt

      • Complex_AUPRC_aeo.txt

      • Complex_AUPRC_gls.txt

      • Complex_AUPRC_olf.txt

    • Diversity data

      • CORUM_complex_Diversity_data_depmap_q2_2020_onion_0.tsv

      • CORUM_complex_Diversity_data_pco.tsv

      • CORUM_complex_Diversity_data_rpco.tsv

      • CORUM_complex_Diversity_data_aeo.tsv

      • CORUM_complex_Diversity_data_gls.tsv

      • CORUM_complex_Diversity_data_olf.tsv

    • Diversity plots

      • CORUM_complex_Diversity_plot_depmap_q2_2020_onion_0.pdf

      • CORUM_complex_Diversity_plot_pco.pdf

      • CORUM_complex_Diversity_plot_rpco.pdf

      • CORUM_complex_Diversity_plot_aeo.pdf

      • CORUM_complex_Diversity_plot_gls.pdf

      • CORUM_complex_Diversity_plot_olf.pdf

    • PR plots

      • depmap_q2_2020_onion_CORUM_complex_PR_.pdf

      • depmap_q2_2020_onion_no_mitoCORUM_complex_PR_.pdf

      • depmap_q2_2020_onion_benchmarkCORUM_complex_PR_.pdf

      • depmap_q2_2020_onion_benchmark_no_mitoCORUM_complex_PR_.pdf

  • AUPRC barplots - analysis results

    • auprc_bar_plot_0.1_0.1_layers_onion.pdf

    • auprc_bar_plot_0.3_0.3_layers_onion.pdf

    • auprc_bar_plot_0.5_0.5_layers_onion.pdf

    • auprc_bar_plot_0.7_0.7_layers_onion.pdf

    • auprc_barplot_onion_0.1_0.1_benchmark.pdf

    • auprc_barplot_onion_0.3_0.3_benchmark.pdf

    • auprc_barplot_onion_0.5_0.5_benchmark.pdf

    • auprc_barplot_onion_0.7_0.7_benchmark.pdf

  • OLF normalized data

    • Normalized_olf_4_scaled.tsv