Construction of the CF signaling network

This repository contains all the scripts and data to reproduce the construction and the analysis of the CF signalling network. The overall network can be accessed as a Cytoscape session, in the sysbio-curie/CFnetwork_cystoscape github repository for further analysis.

Please note that the repository is currently undergoing some cleanup and organization. It may not be in its final, clean state. I'm currently working on making this repository more organized and user-friendly. If you have any questions or suggestions, please don't hesitate to reach out (matthieu dot najm at minesparis dot psl dot eu).

Feel free to explore, run, and adapt these scripts to suit your analysis needs. Explore the following sections to understand the content and purpose of each file:

1. Transcriptomics analyses

1.1 Differential Expression Analysis at the pathway level with fGSEA

Perform pathway-level differential expression analysis with fgsea algorithm for each study.

Conda environment

fgsea

Scripts

- scripts/fgsea/Verhaeghe_fgsea.Rmd
- scripts/fgsea/Ogilvie_nasal_fgsea.Rmd
- scripts/fgsea/Ogilvie_bronchial.Rmd
- scripts/fgsea/Voisin_fgsea.Rmd
- scripts/fgsea/Clarke_fgsea.Rmd
- scripts/fgsea/Balloy_fgsea.Rmd
- scripts/fgsea/Zoso_fgsea.Rmd
- scripts/fgsea/Ling_fgsea.Rmd
- scripts/fgsea/Saint_Criq_fgsea.Rmd

Inputs

Gene level t-statistics:

- data/differential_expression_data/Verhaeghe_DEG_limma_unique_HGNC.txt
- data/differential_expression_data/Ogilvie_nasal_DEG_limma_unique_HGNC.csv
- data/differential_expression_data/Ogilvie_bronchial_DEG_limma_unique_HGNC.csv
- data/differential_expression_data/Voisin_DEG_limma_unique_HGNC.txt
- data/differential_expression_data/Clarke_DEG_limma_unique_HGNC.csv
- data/differential_expression_data/Balloy_without_CTRL2_DEG_limma_unique_HGNC.txt
- data/differential_expression_data/Zoso_DEG_limma_unique_HGNC.txt
- data/differential_expression_data/Saint_Criq_UNC_without_NCF_2_DEG_limma_unique_HGNC.txt
- data/differential_expression_data/Saint_Criq_SC_DEG_limma_unique_HGNC.txt

GMT:

- data/kegg_pathways/kegg_pathways_from_omnipathR.gmt

Outputs

- data/fgsea_output/Verhaeghe_fgsea_report_kegg_pathways.RData
- data/fgsea_output/Ogilvie_nasal_fgsea_report_kegg_pathways.RData
- data/fgsea_output/Ogilvie_bronchial_fgsea_report_kegg_pathways.RData
- data/fgsea_output/Voisin_fgsea_report_kegg_pathways.RData
- data/fgsea_output/Clarke_fgsea_report_kegg_pathways.RData
- data/fgsea_output/Balloy_without_CTRL2_unfiltered_fgsea_report_kegg_pathways.RData
- data/fgsea_output/Zoso_fgsea_report_kegg_pathways.RData
- data/fgsea_output/Ling_unfiltered_fgsea_report_kegg_pathways.RData
- data/fgsea_output/Saint_Criq_UNC_without_NCF_2_fgsea_report_kegg_pathways.RData
- data/fgsea_output/Saint_Criq_SC_fgsea_report_kegg_pathways.RData

1.2 Meta-analysis at the pathway level

Compare the results of the pathway level analysis of all the studies to extract a list of common dysregulated pathways in CF.

Conda environment

deseq

Script

- scripts/fgsea_comparison/fGSEA_comparison.Rmd

Dependencies

- scripts/fgsea_comparison/Fgsea_output_preprocess.R
- scripts/fgsea_comparison/Fgsea_comparison_utils.R

Output

- data/kegg_diff_pathways/fgsea_nes_diff_pathways.RData

2. From pathways to CF Network

Correct and merge the common dysregulated pathways into one single network. Add CFTR and CFTR interactors to the network.

Conda environment

deseq

Script

- scripts/pathways_to_network/kegg_diff_pathways_to_network.Rmd

Input

List of interactions and nodes to correct in KEGG pathways - data/kegg_pathways/kegg_diff_pathways_corrections_w_EZR_2023_07_07.txt

Dependencies

Correction of KEGG pathways

- scripts/kegg_pathways/kegg_pathways_manual_curation.R
- scripts/pathways_to_network/network_utils.R

Add CFTR interactors (Optional)

- scripts/pathways_to_network/CFTR_interactors_helper.R

Outputs

- data/kegg_diff_pathways_network/kegg_diff_pathways_interactions_with_CFTR_interactors_df.RData : CF network interactions as data.frame
- data/kegg_diff_pathways_network/kegg_diff_pathways_nodes_with_CFTR_interactors_df.RData : CF network nodes as data.frame

3. CF network pruning

Network pruning and cleaning (corresponding to the part 3.6 of the Methods section).

Script

- scripts/network_analysis/kegg_diff_pathways_network_layout.R

Input

- data/kegg_diff_pathways_network/kegg_diff_pathways_interactions_with_CFTR_interactors_df.RData : CF network interactions as data.frame
- data/kegg_diff_pathways_network/kegg_diff_pathways_nodes_with_CFTR_interactors_df.RData : CF network nodes as data.frame

Dependencies

- scripts/network_analysis/simplify_network_helper.R 
- scripts/network_analysis/network_visualisation_helper.R

Outputs

- data/kegg_diff_pathways_network/diff_kegg_pathways_with_CFTR_interactors_PPI_direct_tagged_interactions_df.txt : final pruned CF network interactions as txt file.
- data/kegg_diff_pathways_network/diff_kegg_pathways_with_CFTR_interactors_PPI_direct_tagged_nodes_df.txt : final pruned CF network nodes as txt file.

4. CF network analysis

Network topological analysis (corresponding to the part 2.5 of the Results).

Script

- scripts/network_analysis/kegg_diff_pathways_network_analysis_final.R

Input

- data/kegg_diff_pathways_network/diff_kegg_pathways_with_CFTR_interactors_PPI_direct_tagged_interactions_df.txt : final pruned CF network interactions as txt file.
- data/kegg_diff_pathways_network/diff_kegg_pathways_with_CFTR_interactors_PPI_direct_tagged_nodes_df.txt : final pruned CF network nodes as txt file.

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A. Supplementary Analysis

A.1 KEGG Pathways Preprocessing

Conda environment

doro-r4

Script - Retrieve KEGG signaling pathways.

- scripts/kegg_pathways/kegg_pathways_preprocess.R

Outputs

- kegg_pathways/kegg_pathways_from_omnipathR.gmt
- kegg_pathways/kegg_pathwaysKegg_pathways_from_omnipathR.txt
- kegg_pathways/kegg_pathways_from_omnipath_list.Rdata
- kegg_pathways/Kegg_pathways_from_omnipath_nodes_carac.Rdata

Visualisation

- kegg_pathways/example_kegg_pathway.R

A.2 CyFi-MAP Preprocessing

Conda environment

deseq

Script - Extract CFTR interactors from the CyFi database

- scripts/CyFi-MAP_scripts/extract_CyFi_MAP_CFTR_interactors.R 

Inputs

- CyFi-MAP/CFTR_cp17-elementExport_2022_10_26_MN_2.txt : elements of the wt-CFTR interactome. 
- CyFi-MAP/CFTR_cp17-networkExport_2022_10_26.txt: network interactions of the wt-CFTR interactome.
- CyFi-MAP/F508del_cp21-elementExport_MN.txt : elements of the F508del-CFTR interactome. 
- CyFi-MAP/F508del_cp21-networkExport.txt : network interactions of the F508del-CFTR interactome.

Dependencies - Transform complexes to proteins.

- scripts/CyFi-MAP_scripts/CyFi_MAP_helper.R

Outputs

- CFTR_interactors/CFTR_interactors_nodes_df.RData : CFTR interactors extracted from the CyFi-MAP database.
- CFTR_interactors/CFTR_interactors_interactions_df.RData : CFTR interactions extracted from the CyFi-MAP database.

A.3. - Differential Expression Analysis at the gene Level

Script - Compare differentially expressed genes.

- scripts/DEG_comparison/DEG_comparison.Rmd

Dependencies

- scripts/DEG_comparison/deg_utils.R