Build network based on kinase-phosphosite interactions
This notebook provides the code to create a network based on kinase-substrate interactions and the annotated effect of phosphorylation (based on PhosphositePlus) on the activity of the substrate.
[1]:
%%time
from neko.core.network import Network
from neko._visual.visualize_network import NetworkVisualizer
from neko.inputs import Universe, phosphosite
from neko._annotations.gene_ontology import Ontology
import omnipath as op
import pandas as pd
CPU times: user 5.41 s, sys: 1.63 s, total: 7.04 s
Wall time: 5.17 s
1. Specify kinase-substrate interaction file and phosphosite effect annotation
In this example, both files we utilize are from PhosphositePlus.
[2]:
kinase_int_file = ("../neko/_data/Kinase_Substrate_Dataset")
phospho_effect_file = ("../neko/_data/Regulatory_sites")
2. Add interactions as a resource database
The process_psp_interactions function parses the provided files to create an interaction database in the Omnipath format.
[3]:
resources = phosphosite()
3. Define a set of phosphosites we are interested in
[4]:
genes = ['AKT1S1_T246', 'GSK3B_S9', 'AKT1_S473', 'HSPB1_S78', 'HSPB1_S82', 'MAPK14_T180', 'MAPK14_Y182', 'MAP2K1_S218', 'MAP2K1_S222', 'RPS6KA1_S380', 'MTOR_S2448', 'JUN_S63', 'MAPK3_T202', 'MAPK3_Y204']
4. Build network
[5]:
%%time
new_net1 = Network(genes, resources=resources.interactions)
CPU times: user 2.43 s, sys: 156 ms, total: 2.59 s
Wall time: 2.58 s
Note
Neko is based on UniProt IDs. It is still possible to use databases with other IDs, but an error message will appear during the translation progress, as in the example below.
[6]:
%%time
new_net1.complete_connection(algorithm= 'bfs',only_signed=True, connect_with_bias=True)
Error: node GSK3B is not present in the resources database
Error: node GSK3B is not present in the resources database
Error: node TBK1 is not present in the resources database
Error: node TBK1 is not present in the resources database
Error: node AKT1 is not present in the resources database
Error: node AKT1 is not present in the resources database
Error: node AKT1 is not present in the resources database
Error: node MAPK14 is not present in the resources database
Error: node MAPK14 is not present in the resources database
Error: node MAPKAPK2 is not present in the resources database
Error: node MAPKAPK2 is not present in the resources database
Error: node MAPK14 is not present in the resources database
Error: node MAP2K1 is not present in the resources database
Error: node MAP2K1 is not present in the resources database
Error: node MAPK3 is not present in the resources database
Error: node MAPK3 is not present in the resources database
Error: node CDK2 is not present in the resources database
Error: node CDK2 is not present in the resources database
Error: node AKT1 is not present in the resources database
Error: node MAP2K1 is not present in the resources database
Error: node MAP2K1 is not present in the resources database
Error: node MAPK3 is not present in the resources database
Error: node RPS6KA1 is not present in the resources database
Error: node RPS6KA1 is not present in the resources database
Error: node MTOR is not present in the resources database
Error: node MTOR is not present in the resources database
Error: node MAPK3 is not present in the resources database
Error: node AKT1 is not present in the resources database
Error: node TBK1 is not present in the resources database
Error: node GSK3B is not present in the resources database
Error: node SRC is not present in the resources database
Error: node SRC is not present in the resources database
Error: node PDPK1 is not present in the resources database
Error: node PDPK1 is not present in the resources database
Error: node PRKACA is not present in the resources database
Error: node PRKACA is not present in the resources database
Error: node GSK3B is not present in the resources database
Error: node SRC is not present in the resources database
Error: node SRC is not present in the resources database
Error: node PRKD1 is not present in the resources database
Error: node PRKD1 is not present in the resources database
Error: node GSK3B is not present in the resources database
Error: node MAP3K11 is not present in the resources database
Error: node MAP3K11 is not present in the resources database
Error: node MAP2K4 is not present in the resources database
Error: node MAP2K4 is not present in the resources database
Error: node SRC is not present in the resources database
Error: node RET is not present in the resources database
Error: node RET is not present in the resources database
Error: node GSK3B is not present in the resources database
Error: node SRC is not present in the resources database
Error: node SRC is not present in the resources database
Error: node ARAF is not present in the resources database
Error: node ARAF is not present in the resources database
Error: node SRC is not present in the resources database
Error: node RAF1 is not present in the resources database
Error: node RAF1 is not present in the resources database
Error: node SRC is not present in the resources database
Error: node CDK1 is not present in the resources database
Error: node CDK1 is not present in the resources database
Error: node MAPK3 is not present in the resources database
Error: node MAPK3 is not present in the resources database
Error: node AKT1 is not present in the resources database
Error: node PRKD1 is not present in the resources database
Error: node RET is not present in the resources database
CPU times: user 724 ms, sys: 11.1 ms, total: 735 ms
Wall time: 733 ms
[7]:
visualizer1 = NetworkVisualizer(new_net1, color_by='effect')
visualizer1.render()
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