tandreanisanofi / pitzalis_collaboration

Calculation of Gene Module Scores

Gene Module Score to estimate cell type abundance

Calculation of Gene Module Scores from gene expression matrices to characterize the cell type(s) in different patients.

Input (check the folder input)

The function to run
Gene Expression Matrix (bring the one that you have from your samples)
Gene annotation
Cell type of interest (from a list of selected)

Output

A file where rows are patients and column is the cell type. Each value represents the gene module score.

Run the bash script

Example how to run the code on the bash command line:

Rscript Gene_Module.R cell_types_and_genes.txt "Plasmacell" Human.B38_OmicsoftGenCode.V33.Genes.annotation3.txt Pitzalis_R4RA_Blood_All_samples.RnaSeq_Genes.7Outliers_removed.Count.vst_20221121.txt Plasmacell_Gene_module.txt  

Description and exaplanation of the 4 input and 1 output

Rscript is used to run an R script from unix command line while "Gene_Module.R" is the script to run
The 5 main parameters the script takes are:

1. cell_types_and_genes.txt: file in which for each cell type there is a list of gene specific;

2. "Plasmacell": Name of the cell to compute the gene module score, this is a full list (please use the exact word(s) using "":

   • Basophils
   • CD14+ Monocytes
   • CD14+CD16+ Monocytes
   • CD14+CD16- Monocytes
   • CD14-CD16+ Monocytes
   • CD19+ B Cells
   • CD34+ Progenitors
   • CD4+ T Cells
   • CD4+CD25+CD45RA+ naive regulatory T cells
   • CD4+CD25+CD45RA- memory regulatory T cells
   • CD4+CD25-CD45RA+ naive conventional T cells
   • CD4+CD25-CD45RA- memory conventional T cells
   • CD8+ T Cells
   • Dendritic Cells - plasmacytoid
   • Endothelial Cells - Lymphatic
   • Endothelial Cells - Microvascular
   • Eosinophils
   • Fibroblast - skin
   • Mast cell
   • Natural Killer Cells
   • Neutrophils
   • Plasmacell
   • Synoviocyte
   • gamma delta positive T cells

3. Human.B38_OmicsoftGenCode.V33.Genes.annotation3.txt: annotation of the gene's name

4. Gene_Expression_Matrix.txt: Matrix with the gene expression values (row genes, columns Patient Id)

5. Plasmacell_Gene_module.txt: Output with the gene module score for the cell type under investigation for each patient. In the example "Plasmacell" but can be changed according to the cell type in the parameter 2

Visualization Gene modules HeatMap

Check the folder Script HeatMap_GeneModules_R4RA.r

Multi Omics data integration to characterize Responders vs Not Responders patients at baseline treated with biologics

Script to conduct data wrangling, obtain Multi Omics Factor Analysis (MOFA) models and interpretation

Input (check the folder input)

Matrices of:

1. RNA-seq blood
2. RNA-seq synovium
3. Targeted Proteomics Olink
4. Lipidomics
5. Metabolomics

Output

Plot with top features (genes, metabolites, lipids, proteins..) associated with response to treatment.

Script:

Check the folder Script MultiOmics_R_vs_NR_Rituximab.r and MultiOmics_R_vs_NR_Tocilizumab.r.