README

This repository contains the code used for data analysis and figure generation in the study titled "Nuclear Respiratory Factor 1 (NRF1) promotes cell survival in Multiple Myeloma under proteasome inhibition therapy."

The scripts are organized by figure to facilitate reproducibility of the results. Raw data supporting the figures will be made publicly available on the GEO database. If you require access to specific processed datasets, please feel free to contact me via email.

Figure 1

Fig1bdatasetdescription:

Fig1ctfenrichment_heatmap: The R script was executed with the following parameters, and the resulting plot can be found here

r Rscript ./scripts/Figure1c_motif_matrix_heatmap.R -i ./data/matrix_motif_atac_tumour_mgus_0423_groupv2.txt -o ./figures -p heatmap_motifs_score_obs_exp_atac_tumour_mgus_0423_groupv2 -c 3 -store_rc TRUE

Figure1fcorrelationwith_Nilson.md

Figure 2

Fig2eNRF1medianexpressionsurvival: The R script was executed with the following parameters, and the resulting plot can be found here

bash Rscript ./commpass_survival_gene_auto.R -i "NRF1" -r ../COMMPASS_IA17/MMRF_CoMMpass_IA17_salmon_geneUnstranded_tpm.tsv -o ./figures -p survival_commpass_NRF1_median_1123 -surv ../COMMPASS_IA17/CoMMpass_IA17_FlatFiles_0323/MMRF_CoMMpass_IA17_STAND_ALONE_SURVIVAL_V2.tsv -c "CD138pos" -t "median"

Fig2fviolinplottpmsurvivalperiss

Fig2hemissionandtransitionheatmap_chromHMM

Figure 3

Fig3dheatmapatactumourmgus

Fig3fheatmapcelllinesmgus_atac: click here to view the resulting heatmap plot.

Fig3gheatmapchipmgusesordio: click here to view the resulting heatmap plot.

Figure 4

Fig4bgenessignificantlymodulatedduringdiseaseprogressioncommpasspv1_3:

The R script was executed with the following parameters, and the resulting plot can be found here

bash Rscript Fig4/scripts/commpass_for_signature_auto_ensID_2_pv1_3.R -v data/MMRF_CoMMpass_IA17_PER_PATIENT_VISIT_V2.tsv -g data/MMRF_CoMMpass_IA17_PER_PATIENT_V2.tsv -i data/10_master_list_consensus_our_chip_1123_ANNOTATED_selected_TSS_minus_plus_2kb_GENE_NAME.bed -r data/MMRF_CoMMpass_IA17_salmon_geneUnstranded_tpm.tsv -o figures -p compass_progression_10_master_list_consensus_our_chip_1123_ANNOTATED_selected_TSS_minus_plus_2kb -t compass_progression_10_master_list_consensus_our_chip_1123_ANNOTATED_selected_TSS_minus_plus_2kb -c "CD138pos" -s TRUE -S "UP" -sub T

Fig4eFig4fFig4gFig4hNRF1generegualtedsignatureplussurvivalcommpass

Suppl1

Suppl1asaturation_plot

Suppl1btopmakeggbarplot: the R script was executed with the following parameters and the resulting plot can be found here

jsx Rscript make_ggbarplot.r -i data/Suppl/number_of_peaks_per_sample_atac_tumour_mgus_2023.txt -o figures/Suppl -p peaks_for_SI_atac_tumour_mgus_0423.png -x "Filename" -y "NumLines" -pheno data/Suppl/sample_sheet_official_clinical_2023_subsetted_PHENOTYPE.csv -y_lab "Number of peaks" -x_lab ""

Suppl1bbottomcountspeaksSIchecks

Suppl2

Suppl2aCRISPdepmapdependency

Suppl2gNRF1enhancerpromoterenrichmentevaluation

Suppl3

Suppl3aPCAanalysistumourplusmgus: the R script was executed with the following parameters and the resulting plot can be found here

r Rscript PCA_analysis_auto_0124.R -i data/Suppl/matrix_multicov_tumout_and_MGUS_on_tumour_master_list_0124.txt -o figures/Suppl -p "PCA_mgus_plus_tumour_treated_plus_tumour_onset_1224.png" -pheno data/Suppl/sample_sheet_clinical_PHENOTYPE_tumour_and_mgus_0124.txt -labels FALSE

Suppl3bmakeggbarplotMGUSpeaksper_patient: the R script was executed with the following parameters and the resulting plot can be found here

r Rscript make_ggbarplot.r -i data/Suppl/number_of_peaks_per_sample_atac_tumour_mgus_2023_MGUS.txt -o figures -p barplot_num_peaks_MGUS_2023_sel -x "Filename" -y "NumLines" -pheno data/Suppl/sample_sheet_MGUS_PHENOTYPE.txt -y_lab "Number of peaks" -x_lab ""

Suppl4

Suppl4abubbleplotissgenetics

Suppl4bdetectcorrelatedtargetgenefrom_COMMPASS: the R script was executed with the following parameters and the resulting plot can be found here

r Rscript commpass_search_for_correlated_genes_auto_PAPER.R -r data/Suppl/MMRF_CoMMpass_IA17_salmon_geneUnstranded_tpm.tsv -g data/compass_progression_10_master_list_consensus_our_chip_1123_ANNOTATED_selected_TSS_minus_plus_2kb_UP_05_wilcox_OR_ISS_pv1_3_GENE_NAME.txt -o figures -p heatmap_correlation_compass_progression_10_master_list_consensus_our_chip_1123_ANNOTATED_selected_TSS_minus_plus_2kb_UP_05_wilcox_OR_ISS_pv1_3_0124 -R 2 -C 2 -store_rc T -sub T -t UP -title "Correlation of genes increasing-UP during disease progression matching 10_master_list_consensus_our_chip_1123_ANNOTATED_selected_TSS_minus_plus_2kb_UP_05_wilcox_OR_ISS_pv1_3"

Suppl5

Suppl5aleftcommpassheatmapnatureZHAN_signatures

Suppl5arightcommpassheatmapnatureBROYL_signatures

Suppl5bcontingencychisquaregenetics

Suppl5cMultivariate_analysis