kpmp_picaso_data_prep

[1]:

%load_ext autoreload

import os, sys
import networkx as nx

sys.path.insert(0, "../")
sys.path.insert(0, "/home/j/joppich/.local/lib/python3.11/site-packages/")
#otherwise leidenalg is used in an outdated version ...

import leidenalg as la
print("la", la.version)

%autoreload 2
from PICASO.kgraph import *
import pandas as pd
import numpy as np

import matplotlib
import matplotlib.pyplot as plt

from collections import defaultdict, Counter

import random
random.seed(42)

import pickle

la 0.10.1

[2]:

kg = KGraph()
kg.load_kgraph("../data/initial_base_graph.out")

[3]:

exprDF = pd.read_csv("./expression_ctcond_mean_df.tsv", sep="\t")

[4]:

exprDFs = {}

for group in exprDF.group.unique():
    exprDFs[group] = exprDF[exprDF.group == group].copy()

print([x for x in exprDFs])

['ATL_AKI', 'ATL_COV_AKI', 'ATL_DKD', 'ATL_H_CKD', 'ATL_Ref', 'CNT_AKI', 'CNT_COV_AKI', 'CNT_DKD', 'CNT_H_CKD', 'CNT_Ref', 'DCT_AKI', 'DCT_COV_AKI', 'DCT_DKD', 'DCT_H_CKD', 'DCT_Ref', 'DTL_AKI', 'DTL_COV_AKI', 'DTL_DKD', 'DTL_H_CKD', 'DTL_Ref', 'EC_AKI', 'EC_COV_AKI', 'EC_DKD', 'EC_H_CKD', 'EC_Ref', 'FIB_AKI', 'FIB_COV_AKI', 'FIB_DKD', 'FIB_H_CKD', 'FIB_Ref', 'IC_AKI', 'IC_COV_AKI', 'IC_DKD', 'IC_H_CKD', 'IC_Ref', 'IMM_AKI', 'IMM_COV_AKI', 'IMM_DKD', 'IMM_H_CKD', 'IMM_Ref', 'NEU_AKI', 'NEU_COV_AKI', 'NEU_DKD', 'NEU_H_CKD', 'NEU_Ref', 'PC_AKI', 'PC_COV_AKI', 'PC_DKD', 'PC_H_CKD', 'PC_Ref', 'PEC_AKI', 'PEC_COV_AKI', 'PEC_DKD', 'PEC_H_CKD', 'PEC_Ref', 'POD_AKI', 'POD_COV_AKI', 'POD_DKD', 'POD_H_CKD', 'POD_Ref', 'PT_AKI', 'PT_COV_AKI', 'PT_DKD', 'PT_H_CKD', 'PT_Ref', 'PapE_AKI', 'PapE_COV_AKI', 'PapE_DKD', 'PapE_H_CKD', 'PapE_Ref', 'TAL_AKI', 'TAL_COV_AKI', 'TAL_DKD', 'TAL_H_CKD', 'TAL_Ref', 'VSM/P_AKI', 'VSM/P_COV_AKI', 'VSM/P_DKD', 'VSM/P_H_CKD', 'VSM/P_Ref']

[5]:

exprKGs = {}

gsa = GenesetAnnotator()
mNS = MeanNetworkScorer()

for group in exprDFs:

    print(group)

    gKG = KGraph()

    gKG.load_kgraph("../data/initial_base_graph.out")

    gKG.add_gene_expression(exprDFs[group])
    mNS.score_nodes_from_properties(gKG)

    mNS.score(gKG)

    gsa.annotate_genesets(gKG, settype="disease", targettype="gene")
    gsa.annotate_genesets(gKG, settype="geneset", targettype="gene")
    gsa.annotate_genesets(gKG, settype="ncRNA", targettype="gene")
    gsa.annotate_genesets(gKG, settype="drug", targettype=["gene", "disease"])

    exprKGs[group] = gKG

ATL_AKI
Measured Genes 13035
Found Genes 12177

/mnt/raidbio/extproj/projekte/regulatory_networks/kpmp/../mikg/kgraph.py:1621: RuntimeWarning: invalid value encountered in scalar divide
  edge_zscore = (edge_score-etype2mean[etype])/etype2std[etype]

Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
ATL_COV_AKI
Measured Genes 10860
Found Genes 10323
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
ATL_DKD
Measured Genes 7668
Found Genes 7276
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
ATL_H_CKD
Measured Genes 12603
Found Genes 11625
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
ATL_Ref
Measured Genes 25348
Found Genes 20285
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
CNT_AKI
Measured Genes 24853
Found Genes 19978
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
CNT_COV_AKI
Measured Genes 22491
Found Genes 18662
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
CNT_DKD
Measured Genes 21083
Found Genes 17941
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
CNT_H_CKD
Measured Genes 18024
Found Genes 15904
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
CNT_Ref
Measured Genes 24875
Found Genes 20060
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
DCT_AKI
Measured Genes 24805
Found Genes 19999
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
DCT_COV_AKI
Measured Genes 23610
Found Genes 19311
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
DCT_DKD
Measured Genes 21647
Found Genes 18329
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
DCT_H_CKD
Measured Genes 17726
Found Genes 15628
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
DCT_Ref
Measured Genes 24947
Found Genes 20067
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
DTL_AKI
Measured Genes 21441
Found Genes 18050
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
DTL_COV_AKI
Measured Genes 19646
Found Genes 16979
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
DTL_DKD
Measured Genes 21813
Found Genes 18233
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
DTL_H_CKD
Measured Genes 23656
Found Genes 19281
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
DTL_Ref
Measured Genes 26085
Found Genes 20679
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
EC_AKI
Measured Genes 24211
Found Genes 19726
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
EC_COV_AKI
Measured Genes 20951
Found Genes 17893
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
EC_DKD
Measured Genes 23695
Found Genes 19535
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
EC_H_CKD
Measured Genes 23625
Found Genes 19388
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
EC_Ref
Measured Genes 26545
Found Genes 20989
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
FIB_AKI
Measured Genes 25232
Found Genes 20269
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
FIB_COV_AKI
Measured Genes 18476
Found Genes 16361
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
FIB_DKD
Measured Genes 23626
Found Genes 19480
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
FIB_H_CKD
Measured Genes 23097
Found Genes 19077
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
FIB_Ref
Measured Genes 26728
Found Genes 21093
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
IC_AKI
Measured Genes 24370
Found Genes 19757
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
IC_COV_AKI
Measured Genes 22986
Found Genes 19020
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
IC_DKD
Measured Genes 23027
Found Genes 19076
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
IC_H_CKD
Measured Genes 23430
Found Genes 19119
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
IC_Ref
Measured Genes 25871
Found Genes 20617
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
IMM_AKI
Measured Genes 24613
Found Genes 20008
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
IMM_COV_AKI
Measured Genes 21137
Found Genes 18083
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
IMM_DKD
Measured Genes 22849
Found Genes 19145
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
IMM_H_CKD
Measured Genes 22167
Found Genes 18629
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
IMM_Ref
Measured Genes 24843
Found Genes 20135
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
NEU_AKI
Measured Genes 4913
Found Genes 4678
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
NEU_COV_AKI
Measured Genes 2674
Found Genes 2615
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
NEU_DKD
Measured Genes 7374
Found Genes 7107
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
NEU_H_CKD
Measured Genes 5789
Found Genes 5604
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
NEU_Ref
Measured Genes 9914
Found Genes 9408
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PC_AKI
Measured Genes 23050
Found Genes 19001
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PC_COV_AKI
Measured Genes 22158
Found Genes 18483
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PC_DKD
Measured Genes 23520
Found Genes 19283
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PC_H_CKD
Measured Genes 24576
Found Genes 19776
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PC_Ref
Measured Genes 27335
Found Genes 21411
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PEC_AKI
Measured Genes 20644
Found Genes 17531
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PEC_COV_AKI
Measured Genes 18874
Found Genes 16509
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PEC_DKD
Measured Genes 18098
Found Genes 16070
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PEC_H_CKD
Measured Genes 14476
Found Genes 13386
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PEC_Ref
Measured Genes 19920
Found Genes 17116
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
POD_AKI
Measured Genes 21978
Found Genes 18382
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
POD_COV_AKI
Measured Genes 18315
Found Genes 16108
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
POD_DKD
Measured Genes 20558
Found Genes 17636
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
POD_H_CKD
Measured Genes 18157
Found Genes 16017
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
POD_Ref
Measured Genes 22669
Found Genes 18796
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PT_AKI
Measured Genes 26999
Found Genes 21188
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PT_COV_AKI
Measured Genes 25355
Found Genes 20358
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PT_DKD
Measured Genes 27326
Found Genes 21479
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PT_H_CKD
Measured Genes 25527
Found Genes 20426
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PT_Ref
Measured Genes 27242
Found Genes 21332
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PapE_AKI
Measured Genes 1519
Found Genes 1501
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PapE_COV_AKI
Measured Genes 2028
Found Genes 1997
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PapE_DKD
Measured Genes 5000
Found Genes 4804
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PapE_H_CKD
Measured Genes 642
Found Genes 629
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
PapE_Ref
Measured Genes 21401
Found Genes 18078
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
TAL_AKI
Measured Genes 25449
Found Genes 20350
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
TAL_COV_AKI
Measured Genes 26159
Found Genes 20790
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
TAL_DKD
Measured Genes 26114
Found Genes 20801
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
TAL_H_CKD
Measured Genes 26847
Found Genes 21101
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
TAL_Ref
Measured Genes 27434
Found Genes 21436
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
VSM/P_AKI
Measured Genes 20558
Found Genes 17582
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
VSM/P_COV_AKI
Measured Genes 12468
Found Genes 11766
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
VSM/P_DKD
Measured Genes 19803
Found Genes 17229
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
VSM/P_H_CKD
Measured Genes 20301
Found Genes 17431
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']
VSM/P_Ref
Measured Genes 23499
Found Genes 19348
Processed 7884 of 43646 target nodes for settype=disease and targettype=gene
Processed 42878 of 43646 target nodes for settype=geneset and targettype=gene
Processed 3390 of 43646 target nodes for settype=ncRNA and targettype=gene
Processed 3513 of 51488 target nodes for settype=drug and targettype=['gene', 'disease']

[6]:

print(len(exprKGs))
import pickle

with open("ctcond_exprkgs.pickle", 'wb') as f:
    pickle.dump(exprKGs, f)

80

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