Replicating Adebari et al Paper Results

1. Download the PPI file from GRAND.
2. Register for a WebMeV account and download the GBM and LGG data from WebMeV.
3. Download the curated gene set GMT file from Human MSigDB.
4. Download the protein coding genes from GENCODE (basic gene annotation).
5. Run separate_samples.py to separate data into male and female and find overlapping genes, changing the following:
   • gbm_file_path: The path to the GBM expression data.
   • lgg_file_path: The path to the LGG expression data.
   • split_file_dir: The path to the directory where you wish to store the split files.
6. Run concatenate.py to concatenate together the GBM and LGG files.
7. Run NORMALIZED_DATA_CODE.r to normalize the data, changing the following:
   • concatenatedFile: The path to the concatenated file.
   • normalizedFile: The path where you wish to save the normalized file.
8. Run Code_to_filter_by_PCG.r to filter by protein coding gene, changing the following:
   • mappingFile: The path to the protein coding genes.
   • matrixFile: The path to the concatenated data.
   • filteredMatrixFile: The path where you wish to save the filtered data.
9. Run updatecode.py to split the normalized and filtered data into LGG_F, LGG_M, GBM_F, and GBM_M.
   • split_file_dir: The path to the directory where you wish to store the split files.
   • matrix_dir: The path to the file containing the matrix of gene expression levels.
10. Run runpanda.py to run PANDA, changing the following:
    • localDir: The local directory where the motif, PPI, and expression data are stored.
11. Run PercentileMonster.R to run MONSTER, changing the following:
    • localDir: The local directory where the files are stored.
12. Run diffanalysis.R to do pathway analysis changing the following:
    • localDir: The local directory where the files are stored.
    • pathwayDBFile: The pathway file path.
13. Run Diffanalysis_Visuals.R to plot the pathways, changing the following:
    • localDir: The local directory where the files are stored.
14. Run MONSTER_plots.R changing the following:
    • localDir: The local directory where the files are stored.