Biological Pathways

Extract pathways from a Five3 Genomics Pathway database file as a basis for including gene-gene interactions in a model.



In [2]:

    
import os
import pandas as pd



In [3]:

    
# Load the entire pathway database into a dataframe for parsing and extraction
interactions = pd.read_csv("data/pid_120912_pathway.tab", sep="\t", names=["parent", "child", "interaction"])
interactions.head()









    Out[3]:







  
    
      
      parent
      child
      interaction
    
  
  
    
      0
      protein
      1/2-SBSRNA4
      NaN
    
    
      1
      protein
      AADAT
      NaN
    
    
      2
      protein
      AAGAB
      NaN
    
    
      3
      protein
      ACTR6
      NaN
    
    
      4
      protein
      ADAT2
      NaN



In [4]:

    
# interactions.query("interaction=='-a>' | interaction=='-a|'").head()
interactions.query("parent=='abstract'").head()









    Out[4]:







  
    
      
      parent
      child
      interaction
    
  
  
    
      260
      abstract
      Osteosarcoma_(abstract)
      NaN
    
    
      387
      abstract
      viral_genome_expression_(abstract)
      NaN
    
    
      433
      abstract
      DNA_mediated_transformation_(abstract)
      NaN
    
    
      434
      abstract
      positive_regulation_of_cyclin-dependent_protei...
      NaN
    
    
      435
      abstract
      myoblast_fusion_(abstract)
      NaN



In [6]:

    
interactions[interactions['child'].str.contains("apoptosis")][0:20]









    Out[6]:







  
    
      
      parent
      child
      interaction
    
  
  
    
      685
      abstract
      regulation_of_apoptosis_(abstract)
      NaN
    
    
      2866
      abstract
      apoptosis_(abstract)
      NaN
    
    
      4013
      abstract
      positive_regulation_of_anti-apoptosis_(abstract)
      NaN
    
    
      9480
      abstract
      positive_regulation_of_apoptosis_(abstract)
      NaN
    
    
      11138
      abstract
      neuron_apoptosis_(abstract)
      NaN
    
    
      11322
      abstract
      nuclear_fragmentation_during_apoptosis_(abstract)
      NaN
    
    
      12138
      abstract
      DNA_fragmentation_during_apoptosis_(abstract)
      NaN
    
    
      12163
      abstract
      DNA_damage_response_signal_transduction_by_p53...
      NaN
    
    
      14200
      abstract
      induction_of_apoptosis_(abstract)
      NaN
    
    
      15387
      abstract
      negative_regulation_of_apoptosis_(abstract)
      NaN
    
    
      30043
      TP53
      apoptosis_(abstract)
      -a>
    
    
      30060
      TAp73a_(tetramer)_(complex)
      apoptosis_(abstract)
      -a>
    
    
      30096
      JNK1-2_(family)
      apoptosis_(abstract)
      -a|
    
    
      30114
      BAD/BCL-XL_(complex)
      apoptosis_(abstract)
      -a>
    
    
      30188
      Lamins_(cleaved)_(family)
      positive_regulation_of_apoptosis_(abstract)
      -a>
    
    
      30236
      STAT1_(dimer)_(complex)
      apoptosis_(abstract)
      -a>
    
    
      30255
      ZNF274
      neuron_apoptosis_(abstract)
      -a>
    
    
      30355
      MEF2C
      neuron_apoptosis_(abstract)
      -a|
    
    
      30389
      VIM
      apoptosis_(abstract)
      -a>
    
    
      30393
      BAD
      apoptosis_(abstract)
      -a|

	parent	child	interaction
0	protein	1/2-SBSRNA4	NaN
1	protein	AADAT	NaN
2	protein	AAGAB	NaN
3	protein	ACTR6	NaN
4	protein	ADAT2	NaN

	parent	child	interaction
260	abstract	Osteosarcoma_(abstract)	NaN
387	abstract	viral_genome_expression_(abstract)	NaN
433	abstract	DNA_mediated_transformation_(abstract)	NaN
434	abstract	positive_regulation_of_cyclin-dependent_protei...	NaN
435	abstract	myoblast_fusion_(abstract)	NaN

	parent	child	interaction
685	abstract	regulation_of_apoptosis_(abstract)	NaN
2866	abstract	apoptosis_(abstract)	NaN
4013	abstract	positive_regulation_of_anti-apoptosis_(abstract)	NaN
9480	abstract	positive_regulation_of_apoptosis_(abstract)	NaN
11138	abstract	neuron_apoptosis_(abstract)	NaN
11322	abstract	nuclear_fragmentation_during_apoptosis_(abstract)	NaN
12138	abstract	DNA_fragmentation_during_apoptosis_(abstract)	NaN
12163	abstract	DNA_damage_response_signal_transduction_by_p53...	NaN
14200	abstract	induction_of_apoptosis_(abstract)	NaN
15387	abstract	negative_regulation_of_apoptosis_(abstract)	NaN
30043	TP53	apoptosis_(abstract)	-a>
30060	TAp73a_(tetramer)_(complex)	apoptosis_(abstract)	-a>
30096	JNK1-2_(family)	apoptosis_(abstract)	-a\|
30114	BAD/BCL-XL_(complex)	apoptosis_(abstract)	-a>
30188	Lamins_(cleaved)_(family)	positive_regulation_of_apoptosis_(abstract)	-a>
30236	STAT1_(dimer)_(complex)	apoptosis_(abstract)	-a>
30255	ZNF274	neuron_apoptosis_(abstract)	-a>
30355	MEF2C	neuron_apoptosis_(abstract)	-a\|
30389	VIM	apoptosis_(abstract)	-a>
30393	BAD	apoptosis_(abstract)	-a\|