Systems-level design principles of metabolic rewiring in an animal

Description: This repository contains all source codes, necessary input and output data, and raw figures and tables for reproducing all figures and results published in the following study: Xuhang Li#, Hefei Zhang#, Thomas Hodder, Wen Wang, L. Safak Yilmaz, Chad L. Myers, Albertha J.M. Walhout. Systems-level Worm Perturb-Seq reveals design principles of metabolic rewiring. (2025) Nature, in press (# equal contribution) Files: This repository contains the entire project working directory for this publication. To deposit into Zenodo, we have individually zipped each subfolder of the root directory. To reproduce our study, it is advised that one should download the entire Zenodo repository and unzip every zip file to produce the corresponding subfolders. The "root.zip" should be directly unzipped into the root directory of this project (not your system root!!). The recovered working directory should be like this: 10_revision/ 1_QC_dataCleaning/ 2_DE/ 3_imageAnalysis/ 4_networkAnalysis/ 5_GSA/ 7_FBA_modeling/ data_and_tables_to_publish/ input_data/ generate_all_tables_for_publication.R prepareTbls_met12.R prepareTbls_metVali1_OCC.R prepareTbls_metVali2_b12.R prepareTbls_metVali3_detox.R prepareTbls.R prepareTbls_SPECIAL.R REWIRING_FIGURE_LOOKUP.xlsx Please be advised that this repository contains raw codes and data that are not directly related to a figure in our paper. However, they may be useful to generate input used in the analysis of a figure, or to reproduce tables in our manuscript. It may also contain unpublished analyses and figures, which we did not intentionally delete and kept for records. Usage: Please refer to the table in below to locate a specific file for reproducing a figure of interest (also availabe in the REWIRING_FIGURE_LOOKUP.xlsx under the root directory). Figure File Linesa Notes Fig. 1b 1_QC_dataCleaning/5_supplementary_figure_rewiring.R 1-190 Fig. 1c 2_DE/3_1_DE_network_analysis.R 1-83 Fig. 1d 11_additional analysis/special RNAi.R entire file Fig. 1e 2_DE/output/metabolic_GRN_layout2.cys open in Cytoscape Fig. 1f 2_DE/3_1_DE_network_analysis.R 1-71 Fig. 1g 2_DE/3_1_DE_network_analysis.R 1-145 Fig. 2a 2_DE/5_2_coexpression_analysis_direct_tree.R 1-235 Fig. 2b 2_DE/5_1_1_DE_similarity_analysis.R 232-287 Fig. 2c 2_DE/5_1_1_DE_similarity_analysis.R 468-765 For producing the embedding, see "2_DE/clustering_python/cluster_RNAi_UMAP_DBSCAN.ipynb" Fig. 2d 2_DE/5_2_coexpression_analysis_direct_tree.R 136-181 Fig. 2e 2_DE/5_2_coexpression_analysis_direct_tree.R 136-338 Fig. 2f 2_DE/6_2_rewiring_summary_map_PCCtree.R entire file Fig. 3b 2_DE/4_2_pathway_level_analysis.R 2247-2539 Fig. 3c 2_DE/4_2_pathway_level_analysis.R 2247-2506 the published figure uses level 4 and up direction (2_DE/figures/1_pathway_level_analysis/rxn_and_pathway_rewiring_LEVEL4_up.pdf) Fig. 3d 2_DE/4_2_pathway_level_analysis.R 2183-2235 Fig. 3e 2_DE/4_2_pathway_level_analysis.R 1751-2159 Fig. 3g 4_networkAnalysis/2_visualize_example_rewirings.R 803-807 please load the dependency starting from line 1 Fig. 3h 11_additional analysis/glycine tracing/glycine RNAi tracing.R entire file source data also provided along the paper Fig. 3j 4_networkAnalysis/2_visualize_example_rewirings.R 1-601 Fig. 3k 4_networkAnalysis/1_rewiring_network_modules.R entire file Fig. 4a 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_basic_CR_model.R 853-881 run lines 1-100 to load dependency; Euler plot depends on a random seeds; we manually picked one output figure that has best visual representations; see the corresponding Github or "7_FBA_modeling/CR_model_final_run/a1_gene_obj_classification.m" for generating the input matrix (core function matrix) Fig. 4b 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_supp_gspd_1_example_objHeatmap.R entire file Fig. 4c 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_basic_CR_model.R 1-270 Fig. 4d 7_FBA_modeling/CR_model_final_run/3_DEG_modeling_edge_direction_test_randFBA.R, 7_FBA_modeling/CR_model_final_run/3_DEG_modeling_edge_direction_test_randGRN.R entire file Reproducing this figure is complex because it integrates multiple randomization results; search "fitted_CR_interaction_diagram.pdf" or "fitted_CR_interaction_diagram_randGRN.pdf" to locate the code for making the figure (two randomizations, respectively), and track up for a few lines to load the dependency. To fully reproduce the analysis, follow the instructions in the Github and you will need to execute all four files named "3_DEG_modeling_edge_*.R". Fig. 4f 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_supp_fused_with_FBA.R 1-154 numbers are in variable "model_explained" Fig. 4g (left) 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_supp_fused_with_FBA.R entire file corresponding figure produced by lines 342-345 Fig. 4g (right) 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_supp_parameter_sensitivity_fused_with_FBA.R entire file Fig. 5a 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_basic_CR_model.R 1-297 Fig. 5b 7_FBA_modeling/REVISION/human_perturb_seq/3_DEG_modeling_edge_direction_test_randFBA.R entire file and see notes Reproducing this figure is complex because it integrates multiple randomization results; search "fitted_CR_interaction_diagram.pdf" to locate the code for making the figure, and track up for a few lines to load the dependency. To fully reproduce the analysis, follow the instructions in the Github and you will need to execute all two files named "3_DEG_modeling_edge_*.R". Fig. 5c 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_supp_fused_with_FBA.R entire file corresponding figure produced by lines 343-346 Fig. 5d 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_supp_DEG_cutoff_sensitivity_fused_with_FBA.R entire file Extended Data Fig. 1a 1_QC_dataCleaning/5_supplementary_figure_rewiring.R 193-219 Extended Data Fig. 1b 1_QC_dataCleaning/5_supplementary_figure_rewiring.R 1-91 the published figure was remade manually for prettier representations, the plotting function for which is not provided in this code. However, the raw data stays the same. Extended Data Fig. 1c 2_DE/SUPP_extra_figures_for_rewiring.R 280-379 Extended Data Fig. 1d 4_networkAnalysis/s2_rewiring_and_network_GPR.R 387-555 some inputs were generated by "4_networkAnalysis/s2_rewiring_and_network_GPR.m" Extended Data Fig. 1e 4_networkAnalysis/s2_rewiring_and_network_GPR.R 387-555 some inputs were generated by "4_networkAnalysis/s2_rewiring_and_network_GPR.m" Extended Data Fig. 1f 2_DE/4_2_pathway_level_analysis.R 170-257 Extended Data Fig. 1g 2_DE/4_2_pathway_level_analysis.R 170-297 Extended Data Fig. 1h 11_additional analysis/Wormsize/plot for publishing.R entire file Extended Data Fig. 1i 11_additional analysis/Wormsize/plot for publishing.R entire file Extended Data Fig. 2a 2_DE/3_1_DE_network_analysis.R 1-61 Extended Data Fig. 2b 2_DE/3_1_DE_network_analysis.R 1-180 Extended Data Fig. 2c 2_DE/3_1_DE_network_analysis.R 1-152 Extended Data Fig. 2d 2_DE/3_1_DE_network_analysis.R 364-397 Extended Data Fig. 2e 2_DE/3_1_DE_network_analysis.R 364-383 Extended Data Fig. 2f 2_DE/3_1_DE_network_analysis.R 1-264 Extended Data Fig. 2g 5_GSA/1_DE_annotation_pipeline.R 1389-1522 Extended Data Fig. 3 2_DE/5_1_1_DE_similarity_analysis.R 468-765 For producing the embedding, see "2_DE/clustering_python/cluster_RNAi_UMAP_DBSCAN.ipynb" Extended Data Fig. 4a 4_networkAnalysis/s3_rewiring_and_network_connections.R 1-254 Extended Data Fig. 4b 4_networkAnalysis/s3_rewiring_and_network_connections.R 258-303 Extended Data Fig. 4c 2_DE/5_2_coexpression_analysis_direct_tree.R 136-283 Extended Data Fig. 4d 2_DE/SUPP_extra_figures_for_rewiring.R 725-813 Extended Data Fig. 4e 2_DE/5_2_coexpression_analysis_direct_tree.R 136-589 Extended Data Fig. 4f 11_additional analysis/regulators_nhr_sbp_tor_GEP_mGRN.R entire file Extended Data Fig. 5a 2_DE/6_3_scatter_plot_for_each_DEG_cluster_PCCtree.R 1-224 Extended Data Fig. 5b 2_DE/6_3_scatter_plot_for_each_DEG_cluster_PCCtree.R 1-92 Extended Data Fig. 6a 2_DE/6_1_biCluster_heatmaps_PCCtree.R (top row); 2_DE/6_2_rewiring_summary_map_PCCtree.R (bottom row) top row: 210-219; 229-238; bottom row: 1-162; 162-229 These two scripts produced the last two figures in the first row and the first two figures in the second row. The remaining two figures are repetitive with other main/extended data figures, whose source code were specified there Extended Data Fig. 6b 10_revision/2_tissue_expression_analysis.R 1-184 Extended Data Fig. 6c 10_revision/2_tissue_expression_analysis.R 189-319 Extended Data Fig. 6d 10_revision/2_tissue_expression_analysis.R 326-480 Extended Data Fig. 7a-e 2_DE/6_3_scatter_plot_for_each_DEG_cluster_PCCtree.R 1-189 The annotation bar plot is in 2_DE/SUPP_extra_figures_for_rewiring.R lines 394-715 Extended Data Fig. 8a 2_DE/3_1_DE_network_analysis.R 649-753 Extended Data Fig. 8b 2_DE/3_1_DE_network_analysis.R 649-785 Extended Data Fig. 8c 4_networkAnalysis/2_visualize_example_rewirings.R 759-764 Extended Data Fig. 8d 2_DE/4_2_pathway_level_analysis.R 2247-2506 the published figure uses level 4 and up direction (2_DE/figures/1_pathway_level_analysis/rxn_and_pathway_rewiring_LEVEL4_up.pdf) Extended Data Fig. 8e 4_networkAnalysis/2_visualize_example_rewirings.R 803-807 please load the dependency starting from line 1 Extended Data Fig. 8f 4_networkAnalysis/2_visualize_example_rewirings.R 870-874 please load the dependency starting from line 1 Extended Data Fig. 8g 11_additional analysis/uPhe tracing/uphe RNAi.R entire file source data also provided along the paper Extended Data Fig. 9a 4_networkAnalysis/2_visualize_example_rewirings.R 1-601 Extended Data Fig. 9b 4_networkAnalysis/2_visualize_example_rewirings.R 691-714 please load the dependency starting from line 1 Extended Data Fig. 9c 11_additional analysis/uGlucose tracing/uGlu rewiring.R entire file source data also provided along the paper Extended Data Fig. 9d 4_networkAnalysis/2_visualize_example_rewirings.R 607-629 please load the dependency starting from line 1 Extended Data Fig. 9e 4_networkAnalysis/2_visualize_example_rewirings.R 636-685 Extended Data Fig. 9f 4_networkAnalysis/1_rewiring_network_modules.R entire file Extended Data Fig. 10a 2_DE/6_2_rewiring_summary_map_PCCtree.R entire file This figure is a subset of fig. 2f Extended Data Fig. 10c 7_FBA_modeling/REVISION/1_cluster_CR_model.R entire file Extended Data Fig. 11a 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_supp_excludeMultiObjGenes.R entire file Extended Data Fig. 11b 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_supp_fused_with_FBA.R 1-225 Extended Data Fig. 11c 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_supp_fused_with_FBA.R entire file corresponding figure produced by lines 337-340 Extended Data Fig. 11d 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_supp_fused_with_FBA.R entire file corresponding figure produced by lines 352-355 Extended Data Fig. 11e 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_supp_fused_with_FBA.R entire file corresponding figure produced by lines 362-365 Extended Data Fig. 11f 10_revision/2_tissue_expression_analysis.R 486-742 Extended Data Fig. 12a 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_basic_CR_model.R 300-329 run lines 1-101 to load dependency; Euler plot depends on a random seeds; we manually picked one output figure that has best visual representations; see the corresponding Github or "7_FBA_modeling/REVISION/human_perturb_seq/a1_gene_obj_classification.m" for generating the input matrix (core function matrix) Extended Data Fig. 12b 7_FBA_modeling/REVISION/human_perturb_seq/1_EDA_of_human_perturb_seq.R 1-176 Extended Data Fig. 12c 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_basic_CR_model.R 1-297 Extended Data Fig. 12d 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_basic_CR_model.R 1-297 Extended Data Fig. 12e 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_supp_fused_with_FBA.R 1-224 Extended Data Fig. 12f 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_supp_fused_with_FBA.R entire file corresponding figure produced by lines 337-341 Extended Data Fig. 12g 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_supp_fused_with_FBA.R entire file corresponding figure produced by lines 353-356 Extended Data Fig. 12h 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_supp_fused_with_FBA.R entire file corresponding figure produced by lines 363-366 Extended Data Fig. 12i 7_FBA_modeling/REVISION/human_perturb_seq/2_DEG_modeling_supp_parameter_sensitivity_fused_with_FBA.R entire file Supplementary Data Fig. 2a 2_DE/5_1_1_DE_similarity_analysis.R 467-572 Supplementary Data Fig. 2b 2_DE/6_4_Wald_heatmap_each_RNAi_Cluster.R entire file Supplementary Data Fig. 2c 2_DE/5_1_2_DE_cluster_justification.R 1-389 Supplementary Data Fig. 2d 2_DE/5_1_2_DE_cluster_justification.R 1-308 Supplementary Data Fig. 2e 2_DE/5_1_2_DE_cluster_justification.R 1-234 Supplementary Data Fig. 2f 12_FLEX_benchmark/run_FLEX_eval.sh entire file the bash scripts calls corresponding R scripts for reproducing the figures. You will need to install the FLEX package to run these codes. Supplementary Data Fig. 3, 4 N/A N/A No coding involved as these figures were made manually Supplementary Data Fig. 5 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_basic_CR_model.R 1-270 Supplementary Data Fig. 6 7_FBA_modeling/CR_model_final_run/2_DEG_modeling_basic_CR_model.R 274-578 please load the dependency starting from line 1 a: The lines indicate the chunk of codes to reproduce the corresponding figure; The figure is reproduced at the end of the referred codes. Please note that you may have to run the codes above the referred chunk (i.e., from the first line) to load dependent variables to execute the referred codes. However, you should be able to reproduce the figure only with the codes within the referred script. Notice: We advise you download the entire project working directory (including all zip files and unzip them into corresponding folders), for reproducing any analysis. If you only download the zip file relevant to your figure of interest, you may or may not run into issues due to the missing files in another folder. Contact: For any questions, please contact Xuhang (Hang) Li at [e-mail]. (we plan to deposit an updated version with better code annotations, but cannot complete that currently due to time restirctions)