Investigation of patient specific pathway activities

Sensitivity analysis

• Calculate sensitivity coefficients by varying the amount of each nonzero species

  import os
  from pathlib import Path
  
  from pasmopy import PatientModelAnalyses
  
  import models.breast
  
  
  TNBC_ID = [
      l.strip() for l in Path("models", "breast", "selected_tnbc.txt").read_text("utf-8").splitlines()
  ]
  analyses = PatientModelAnalyses(
      models.breast.__package__,
      TNBC_ID,
      biomass_kws={
          "metric": "maximum", "style": "heatmap", "options": {"excluded_initials": ["PIP2"]}
      },
  )
  analyses.run()
  

Drug response data analysis

1. Calculation of the ErbB receptor expression ratio

   $ cd drug_response
   $ Rscript data/calc_erbb_ratio.R
   

2. Drug response analysis and visualization

   import os
   
   import pandas as pd
   from drug.database import CancerCellLineEncyclopedia
   
   
   ccle = CancerCellLineEncyclopedia()
   
   erbb_expression_ratio = pd.read_csv(
       os.path.join("data", "ErbB_expression_ratio.csv"),
       index_col=0
   )
   compounds = ["Erlotinib", "Lapatinib", "AZD6244", "PD-0325901"]
   for compound in compounds:
       ccle.save_all(erbb_expression_ratio, compound)