Table of Contents

In [1]:

    

import pandas as pd


    

In [2]:

    

quants = pd.read_csv('../output/temp_files/DE_genes.csv')
hypoxia = pd.read_csv('../output/temp_files/hypoxia_response.csv')
hifoh = pd.read_csv('../output/temp_files/hifoh_candidates.csv')
vhl = pd.read_csv('../output/temp_files/vhl_1_regulated_genes.csv')


    

In [3]:

    

hypoxia = hypoxia.target_id.unique()
hifoh = hifoh.target_id.unique()
vhl = vhl.target_id.unique()


    

In [4]:

    

pathway = {}
for gid in hypoxia:
    pathway[gid] = 'hypoxia'
for gid in vhl:
    pathway[gid] = 'vhl'

hOH = {}
for gid in hifoh:
    hOH[gid] = 'non-canonical'


    

In [5]:

    

quants['pathway'] = quants.target_id.map(pathway)


    

In [6]:

    

quants['non_canonical_epistasis'] = quants.target_id.map(hOH)


    

In [7]:

    

quants.head()


    

    
Out[7]:






  

    

      

      
ens_gene
      
ext_gene
      
target_id
      
b
      
se_b
      
qval
      
genotype
      
sorter
      
code
      
pathway
      
non_canonical_epistasis
    
  
  

    

      
0
      
WBGene00007064
      
2RSSE.1
      
2RSSE.1a
      
0.150147
      
0.829418
      
1.000000
      
fog-2
      
5
      
g
      
NaN
      
NaN
    
    

      
1
      
WBGene00007065
      
pot-3
      
3R5.1a
      
0.063856
      
1.909284
      
1.000000
      
fog-2
      
5
      
g
      
NaN
      
NaN
    
    

      
2
      
WBGene00007065
      
pot-3
      
3R5.1b
      
0.274498
      
1.268484
      
1.000000
      
fog-2
      
5
      
g
      
NaN
      
NaN
    
    

      
3
      
WBGene00004964
      
spe-10
      
AC3.10
      
0.197351
      
0.453000
      
0.998032
      
fog-2
      
5
      
g
      
NaN
      
NaN
    
    

      
4
      
WBGene00007070
      
ugt-49
      
AC3.2
      
-0.340556
      
0.140666
      
0.100833
      
fog-2
      
5
      
g
      
NaN
      
NaN
    
  

In [8]:

    

quants = quants[['ens_gene', 'ext_gene', 'target_id', 'b', 'se_b', 'qval', 'genotype', 'pathway', 'non_canonical_epistasis']]
quants = quants[quants.genotype != 'fog-2']
quants.to_csv('../output/supplementary_tables/supplementary_file_1.csv', index=False)