Build network using user-defined resources
This notebook explores how to add other individual resources from Omnipath or other public databases.
[14]:
%%time
from neko.core.network import Network
from neko._visual.visualize_network import NetworkVisualizer
from neko._inputs.resources import Resources
from neko._annotations.gene_ontology import Ontology
import omnipath as op
CPU times: user 28 µs, sys: 0 ns, total: 28 µs
Wall time: 33.9 µs
1. Adding a resource already in Omnipath
1A. Specify the interaction resource of interest
[2]:
extra = op.interactions.LigRecExtra.get()
1B. Add new resource to the Resources object
[3]:
resources = Resources()
resources.add_database(extra, reset_index=True)
WARNING:root:The incoming database is missing some required columns: {'form_complex'}
WARNING:root:This might lead to issues in running the package.
2. Adding a public database
Alternatively, the user might want to use their own interaction databases. We have already implemented the inclusion of some of widely used databases.
As example, we show here how to integrate the Signor 3.0 database. In order to do so, the User needs to have already downloaded the whole Signor database, available at the following link: https://signor.uniroma2.it/downloads.php or with the following code:.
2A. Add Signor database
[4]:
from urllib.request import urlretrieve
url = "https://signor.uniroma2.it/getData.php?organism=9606"
urlretrieve(url, "singor_db.tsv")
[4]:
('singor_db.tsv', <http.client.HTTPMessage at 0x7f7086973730>)
[6]:
resources = Resources()
resources.import_signor_tsv("all_data_08_04_24.tsv") # this function accept only tab separated values
Note
SIGNOR uses has different identifiers for complexes, protein family, phenotype, etc. It is possible that the network contains nodes names like “Signor_pf32” or something like this… This is not yet translated, but if you are interested in what those nodes consist of, you can use download their vocabulary for the entities: https://signor.uniroma2.it/downloads.php
3. Build the network
3A. Import genes as network nodes
[8]:
genes = ["SRC", "NOTCH1", "FAK", "CDH1", "CDH2", "VIM", "MAP4K4", "LATS1", "LATS2", "PTK2B"]
3B. Create network object by specifying the interaction resources
[9]:
new_net1 = Network(genes, resources = resources.interactions)
[10]:
#Print node dataframe
new_net1.nodes
[10]:
| Genesymbol | Uniprot | Type | |
|---|---|---|---|
| 0 | SRC | P12931 | NaN |
| 1 | NOTCH1 | P46531 | NaN |
| 2 | PTK2 | Q05397 | NaN |
| 3 | CDH1 | P12830 | NaN |
| 4 | CDH2 | P19022 | NaN |
| 5 | VIM | P08670 | NaN |
| 6 | MAP4K4 | O95819 | NaN |
| 7 | LATS1 | O95835 | NaN |
| 8 | LATS2 | Q9NRM7 | NaN |
| 9 | PTK2B | Q14289 | NaN |
3C. Build network
The downstream steps to connect your nodes, are the same. Please see the Network building tutorial for detailed explanations of each step.
[11]:
%%time
new_net1.connect_nodes(only_signed=True, consensus_only=True)
CPU times: user 426 ms, sys: 0 ns, total: 426 ms
Wall time: 426 ms
[ ]:
visualizer = NetworkVisualizer(new_net1, color_by='effect')
visualizer.render()
Note
NB! It is important to note, that not all the databases have the same structure as Omnipath. In particular, if the columns “consensus” are missing, we suggest to avoid to use the flag consensus or consensus_only when using Omniflow with customize databases.
[12]:
%%time
new_net1.complete_connection(maxlen=6, k_mean="tight", only_signed=True,
connect_node_when_first_introduced=True) # here, consensus_only is missing, in this way it is automatically False
looking for paths in the network with length: 0 for node SRC and NOTCH1
looking for paths in the network with length: 1 for node SRC and NOTCH1
looking for paths in the network with length: 2 for node SRC and NOTCH1
looking for paths in the network with length: 3 for node SRC and NOTCH1
looking for paths in the network with length: 4 for node SRC and NOTCH1
looking for paths in the network with length: 5 for node SRC and NOTCH1
looking for paths in the network with length: 6 for node SRC and NOTCH1
i_search = 3
Looking for paths with length: 0 for node SRC and NOTCH1
i_search = 3
Looking for paths with length: 1 for node SRC and NOTCH1
i_search = 3
Looking for paths with length: 2 for node SRC and NOTCH1
[['SRC', 'CTNNB1', 'NOTCH1'], ['SRC', 'DAB1', 'NOTCH1']]
P12931 P35222
P35222 P46531
P12931 O75553
O75553 P46531
P12931 Q05397
P12931 P12830
P12931 P19022
P12931 Q14289
P12931 P35222
P12931 O75553
P35222 P46531
O75553 P46531
Q14289 Q05397
P12830 P35222
P19022 P35222
looking for paths in the network with length: 0 for node SRC and PTK2
looking for paths in the network with length: 1 for node SRC and PTK2
Found a path!
[['SRC', 'PTK2']]
looking for paths in the network with length: 0 for node SRC and CDH1
looking for paths in the network with length: 1 for node SRC and CDH1
Found a path!
[['SRC', 'CDH1']]
looking for paths in the network with length: 0 for node SRC and CDH2
looking for paths in the network with length: 1 for node SRC and CDH2
Found a path!
[['SRC', 'CDH2']]
looking for paths in the network with length: 0 for node SRC and VIM
looking for paths in the network with length: 1 for node SRC and VIM
looking for paths in the network with length: 2 for node SRC and VIM
looking for paths in the network with length: 3 for node SRC and VIM
looking for paths in the network with length: 4 for node SRC and VIM
looking for paths in the network with length: 5 for node SRC and VIM
looking for paths in the network with length: 6 for node SRC and VIM
i_search = 3
Looking for paths with length: 0 for node SRC and VIM
i_search = 3
Looking for paths with length: 1 for node SRC and VIM
i_search = 3
Looking for paths with length: 2 for node SRC and VIM
[['SRC', 'PAK2', 'VIM'], ['SRC', 'AKT1', 'VIM'], ['SRC', 'SIGNOR-PF24', 'VIM']]
P12931 Q13177
Q13177 P08670
P12931 P31749
P31749 P08670
P12931 SIGNOR-PF24
SIGNOR-PF24 P08670
P12931 Q05397
P12931 P12830
P12931 P19022
P12931 Q14289
P12931 P35222
P12931 O75553
P12931 Q13177
P12931 P31749
P12931 SIGNOR-PF24
P35222 P46531
O75553 P46531
Q14289 Q05397
P12830 P35222
P19022 P35222
Q13177 P08670
P31749 P08670
SIGNOR-PF24 P08670
P31749 P35222
SIGNOR-PF24 P35222
looking for paths in the network with length: 0 for node SRC and MAP4K4
looking for paths in the network with length: 1 for node SRC and MAP4K4
looking for paths in the network with length: 2 for node SRC and MAP4K4
looking for paths in the network with length: 3 for node SRC and MAP4K4
looking for paths in the network with length: 4 for node SRC and MAP4K4
looking for paths in the network with length: 5 for node SRC and MAP4K4
looking for paths in the network with length: 6 for node SRC and MAP4K4
i_search = 3
Looking for paths with length: 0 for node SRC and MAP4K4
i_search = 3
Looking for paths with length: 1 for node SRC and MAP4K4
i_search = 3
Looking for paths with length: 2 for node SRC and MAP4K4
i_search = 3
Looking for paths with length: 3 for node SRC and MAP4K4
looking for paths in the network with length: 0 for node SRC and LATS1
looking for paths in the network with length: 1 for node SRC and LATS1
looking for paths in the network with length: 2 for node SRC and LATS1
looking for paths in the network with length: 3 for node SRC and LATS1
looking for paths in the network with length: 4 for node SRC and LATS1
looking for paths in the network with length: 5 for node SRC and LATS1
looking for paths in the network with length: 6 for node SRC and LATS1
i_search = 3
Looking for paths with length: 0 for node SRC and LATS1
i_search = 3
Looking for paths with length: 1 for node SRC and LATS1
i_search = 3
Looking for paths with length: 2 for node SRC and LATS1
i_search = 3
Looking for paths with length: 3 for node SRC and LATS1
[['SRC', 'PPP2CA', 'SIGNOR-PF41', 'LATS1'], ['SRC', 'PPP2CA', 'STK3', 'LATS1'], ['SRC', 'PPP2CA', 'STK4', 'LATS1'], ['SRC', 'CFL1', 'SIGNOR-PH18', 'LATS1'], ['SRC', 'CDKN1B', 'CDK1', 'LATS1'], ['SRC', 'ABL1', 'SIGNOR-PF41', 'LATS1'], ['SRC', 'ABL1', 'STK3', 'LATS1'], ['SRC', 'ABL1', 'STK4', 'LATS1'], ['SRC', 'RAF1', 'SIGNOR-PF41', 'LATS1'], ['SRC', 'RAF1', 'STK4', 'LATS1'], ['SRC', 'RAF1', 'STK3', 'LATS1'], ['SRC', 'SIGNOR-PF43', 'VEPH1', 'LATS1'], ['SRC', 'PAK2', 'NF2', 'LATS1'], ['SRC', 'AKT1', 'NUAK1', 'LATS1'], ['SRC', 'AKT1', 'STK3', 'LATS1'], ['SRC', 'AKT1', 'STK4', 'LATS1'], ['SRC', 'AKT1', 'SIGNOR-PF41', 'LATS1'], ['SRC', 'AKT1', 'PRKACA', 'LATS1'], ['SRC', 'RHOA', 'SIGNOR-PH18', 'LATS1'], ['SRC', 'SIGNOR-PF24', 'NUAK1', 'LATS1'], ['SRC', 'SIGNOR-PF24', 'STK3', 'LATS1'], ['SRC', 'SIGNOR-PF24', 'STK4', 'LATS1'], ['SRC', 'SIGNOR-PF24', 'SIGNOR-PF41', 'LATS1'], ['SRC', 'SIGNOR-PF24', 'PRKACA', 'LATS1'], ['SRC', 'GSN', 'SIGNOR-PH18', 'LATS1']]
P12931 P67775
P67775 SIGNOR-PF41
SIGNOR-PF41 O95835
P12931 P67775
P67775 Q13188
Q13188 O95835
P12931 P67775
P67775 Q13043
Q13043 O95835
P12931 P23528
P23528 SIGNOR-PH18
SIGNOR-PH18 O95835
P12931 P46527
P46527 P06493
P06493 O95835
P12931 P00519
P00519 SIGNOR-PF41
SIGNOR-PF41 O95835
P12931 P00519
P00519 Q13188
Q13188 O95835
P12931 P00519
P00519 Q13043
Q13043 O95835
P12931 P04049
P04049 SIGNOR-PF41
SIGNOR-PF41 O95835
P12931 P04049
P04049 Q13043
Q13043 O95835
P12931 P04049
P04049 Q13188
Q13188 O95835
P12931 SIGNOR-PF43
SIGNOR-PF43 Q14D04
Q14D04 O95835
P12931 Q13177
Q13177 P35240
P35240 O95835
P12931 P31749
P31749 O60285
O60285 O95835
P12931 P31749
P31749 Q13188
Q13188 O95835
P12931 P31749
P31749 Q13043
Q13043 O95835
P12931 P31749
P31749 SIGNOR-PF41
SIGNOR-PF41 O95835
P12931 P31749
P31749 P17612
P17612 O95835
P12931 P61586
P61586 SIGNOR-PH18
SIGNOR-PH18 O95835
P12931 SIGNOR-PF24
SIGNOR-PF24 O60285
O60285 O95835
P12931 SIGNOR-PF24
SIGNOR-PF24 Q13188
Q13188 O95835
P12931 SIGNOR-PF24
SIGNOR-PF24 Q13043
Q13043 O95835
P12931 SIGNOR-PF24
SIGNOR-PF24 SIGNOR-PF41
SIGNOR-PF41 O95835
P12931 SIGNOR-PF24
SIGNOR-PF24 P17612
P17612 O95835
P12931 P06396
P06396 SIGNOR-PH18
SIGNOR-PH18 O95835
P12931 Q05397
P12931 P12830
P12931 P19022
P12931 Q14289
P12931 P35222
P12931 O75553
P12931 Q13177
P12931 P31749
P12931 SIGNOR-PF24
P12931 P67775
P67775 P12931
P12931 P23528
P12931 P46527
P12931 P00519
P12931 P04049
P12931 SIGNOR-PF43
P17612 P12931
P12931 P61586
P12931 P06396
P35222 P46531
O75553 P46531
Q14289 Q05397
P12830 P35222
P19022 P35222
Q13177 P08670
P31749 P08670
SIGNOR-PF24 P08670
P06493 P08670
P17612 P08670
SIGNOR-PF41 O95835
Q13188 O95835
Q13043 O95835
SIGNOR-PH18 O95835
P06493 O95835
O95835 Q14D04
Q14D04 O95835
P35240 O95835
O60285 O95835
P17612 O95835
SIGNOR-PF41 Q9NRM7
Q13188 Q9NRM7
Q13043 Q9NRM7
SIGNOR-PH18 Q9NRM7
Q9NRM7 Q14D04
Q14D04 Q9NRM7
P35240 Q9NRM7
P17612 Q9NRM7
P31749 P35222
SIGNOR-PF24 P35222
P67775 P35222
P17612 P35222
Q13177 P00519
Q13177 P35240
P67775 P31749
P31749 SIGNOR-PF41
P31749 Q13188
P31749 Q13043
P31749 P46527
P31749 P04049
P31749 O60285
P31749 P17612
P67775 SIGNOR-PF24
SIGNOR-PF24 SIGNOR-PF41
SIGNOR-PF24 Q13188
SIGNOR-PF24 Q13043
SIGNOR-PF24 P46527
SIGNOR-PF24 P04049
SIGNOR-PF24 O60285
SIGNOR-PF24 P17612
P67775 SIGNOR-PF41
P67775 Q13188
P67775 Q13043
P67775 P04049
SIGNOR-PF41 P00519
P00519 SIGNOR-PF41
P04049 SIGNOR-PF41
P35240 SIGNOR-PF41
Q13188 P00519
P00519 Q13188
P04049 Q13188
Q13188 SIGNOR-PF43
P35240 Q13188
Q13043 P00519
P00519 Q13043
P04049 Q13043
Q13043 SIGNOR-PF43
P35240 Q13043
P23528 SIGNOR-PH18
SIGNOR-PH18 SIGNOR-PF43
P61586 SIGNOR-PH18
P06396 SIGNOR-PH18
P46527 P06493
P06493 P46527
P00519 P46527
P17612 P04049
SIGNOR-PF43 Q14D04
Q14D04 SIGNOR-PF43
P35240 SIGNOR-PF43
P17612 SIGNOR-PF43
P17612 P35240
P17612 P61586
looking for paths in the network with length: 0 for node SRC and LATS2
looking for paths in the network with length: 1 for node SRC and LATS2
looking for paths in the network with length: 2 for node SRC and LATS2
looking for paths in the network with length: 3 for node SRC and LATS2
Found a path!
[['SRC', 'ABL1', 'SIGNOR-PF41', 'LATS2'], ['SRC', 'ABL1', 'STK3', 'LATS2'], ['SRC', 'ABL1', 'STK4', 'LATS2'], ['SRC', 'RAF1', 'SIGNOR-PF41', 'LATS2'], ['SRC', 'RAF1', 'STK4', 'LATS2'], ['SRC', 'RAF1', 'STK3', 'LATS2'], ['SRC', 'SIGNOR-PF24', 'PRKACA', 'LATS2'], ['SRC', 'SIGNOR-PF24', 'SIGNOR-PF41', 'LATS2'], ['SRC', 'SIGNOR-PF24', 'STK4', 'LATS2'], ['SRC', 'SIGNOR-PF24', 'STK3', 'LATS2'], ['SRC', 'PAK2', 'NF2', 'LATS2'], ['SRC', 'SIGNOR-PF43', 'VEPH1', 'LATS2'], ['SRC', 'CFL1', 'SIGNOR-PH18', 'LATS2'], ['SRC', 'GSN', 'SIGNOR-PH18', 'LATS2'], ['SRC', 'AKT1', 'PRKACA', 'LATS2'], ['SRC', 'AKT1', 'SIGNOR-PF41', 'LATS2'], ['SRC', 'AKT1', 'STK4', 'LATS2'], ['SRC', 'AKT1', 'STK3', 'LATS2'], ['SRC', 'RHOA', 'SIGNOR-PH18', 'LATS2'], ['SRC', 'PPP2CA', 'SIGNOR-PF41', 'LATS2'], ['SRC', 'PPP2CA', 'STK4', 'LATS2'], ['SRC', 'PPP2CA', 'STK3', 'LATS2']]
looking for paths in the network with length: 0 for node SRC and PTK2B
looking for paths in the network with length: 1 for node SRC and PTK2B
Found a path!
[['SRC', 'PTK2B']]
looking for paths in the network with length: 0 for node NOTCH1 and PTK2
looking for paths in the network with length: 1 for node NOTCH1 and PTK2
looking for paths in the network with length: 2 for node NOTCH1 and PTK2
looking for paths in the network with length: 3 for node NOTCH1 and PTK2
looking for paths in the network with length: 4 for node NOTCH1 and PTK2
looking for paths in the network with length: 5 for node NOTCH1 and PTK2
looking for paths in the network with length: 6 for node NOTCH1 and PTK2
i_search = 3
Looking for paths with length: 0 for node NOTCH1 and PTK2
i_search = 3
Looking for paths with length: 1 for node NOTCH1 and PTK2
i_search = 3
Looking for paths with length: 2 for node NOTCH1 and PTK2
i_search = 3
Looking for paths with length: 3 for node NOTCH1 and PTK2
[['NOTCH1', 'ERBB2', 'EGFR', 'PTK2'], ['NOTCH1', 'PPARG', 'PTEN', 'PTK2']]
P46531 P04626
P04626 P00533
P00533 Q05397
P46531 P37231
P37231 P60484
P60484 Q05397
P12931 Q05397
P12931 P12830
P12931 P19022
P12931 Q14289
P12931 P35222
P12931 O75553
P12931 Q13177
P12931 P31749
P12931 SIGNOR-PF24
P12931 P67775
P67775 P12931
P12931 P23528
P12931 P46527
P12931 P00519
P12931 P04049
P12931 SIGNOR-PF43
P17612 P12931
P12931 P61586
P12931 P06396
P12931 P00533
P12931 P60484
P35222 P46531
O75553 P46531
P46531 P04626
P46531 P37231
Q14289 Q05397
P00533 Q05397
P60484 Q05397
P12830 P35222
P19022 P35222
Q13177 P08670
P31749 P08670
SIGNOR-PF24 P08670
P06493 P08670
P17612 P08670
SIGNOR-PF41 O95835
Q13188 O95835
Q13043 O95835
SIGNOR-PH18 O95835
P06493 O95835
O95835 Q14D04
Q14D04 O95835
P35240 O95835
O60285 O95835
P17612 O95835
SIGNOR-PF41 Q9NRM7
Q13188 Q9NRM7
Q13043 Q9NRM7
SIGNOR-PH18 Q9NRM7
Q9NRM7 Q14D04
Q14D04 Q9NRM7
P35240 Q9NRM7
P17612 Q9NRM7
P31749 P35222
SIGNOR-PF24 P35222
P67775 P35222
P17612 P35222
P35222 P37231
P37231 P35222
Q13177 P00519
Q13177 P35240
P67775 P31749
P31749 SIGNOR-PF41
P31749 Q13188
P31749 Q13043
P31749 P46527
P31749 P04049
P31749 O60285
P31749 P17612
P60484 P31749
P67775 SIGNOR-PF24
SIGNOR-PF24 SIGNOR-PF41
SIGNOR-PF24 Q13188
SIGNOR-PF24 Q13043
SIGNOR-PF24 P46527
SIGNOR-PF24 P04049
SIGNOR-PF24 O60285
SIGNOR-PF24 P17612
P60484 SIGNOR-PF24
P67775 SIGNOR-PF41
P67775 Q13188
P67775 Q13043
P67775 P04049
SIGNOR-PF41 P00519
P00519 SIGNOR-PF41
P04049 SIGNOR-PF41
P35240 SIGNOR-PF41
Q13188 P00519
P00519 Q13188
P04049 Q13188
Q13188 SIGNOR-PF43
P35240 Q13188
Q13043 P00519
P00519 Q13043
P04049 Q13043
Q13043 SIGNOR-PF43
P35240 Q13043
P23528 SIGNOR-PH18
SIGNOR-PH18 SIGNOR-PF43
P61586 SIGNOR-PH18
P06396 SIGNOR-PH18
P46527 P06493
P06493 P46527
P00519 P46527
P04626 P06493
P06493 P00533
P00519 P00533
P00519 P37231
P17612 P04049
SIGNOR-PF43 Q14D04
Q14D04 SIGNOR-PF43
P35240 SIGNOR-PF43
P17612 SIGNOR-PF43
P17612 P35240
P17612 P61586
P17612 P04626
P17612 P37231
P04626 P00533
P00533 P04626
P37231 P60484
looking for paths in the network with length: 0 for node NOTCH1 and CDH1
looking for paths in the network with length: 1 for node NOTCH1 and CDH1
looking for paths in the network with length: 2 for node NOTCH1 and CDH1
Found a path!
[['NOTCH1', 'CTNNB1', 'CDH1']]
looking for paths in the network with length: 0 for node NOTCH1 and CDH2
looking for paths in the network with length: 1 for node NOTCH1 and CDH2
looking for paths in the network with length: 2 for node NOTCH1 and CDH2
Found a path!
[['NOTCH1', 'CTNNB1', 'CDH2']]
looking for paths in the network with length: 0 for node NOTCH1 and VIM
looking for paths in the network with length: 1 for node NOTCH1 and VIM
looking for paths in the network with length: 2 for node NOTCH1 and VIM
looking for paths in the network with length: 3 for node NOTCH1 and VIM
Found a path!
[['NOTCH1', 'ERBB2', 'CDK1', 'VIM']]
looking for paths in the network with length: 0 for node NOTCH1 and MAP4K4
looking for paths in the network with length: 1 for node NOTCH1 and MAP4K4
looking for paths in the network with length: 2 for node NOTCH1 and MAP4K4
looking for paths in the network with length: 3 for node NOTCH1 and MAP4K4
looking for paths in the network with length: 4 for node NOTCH1 and MAP4K4
looking for paths in the network with length: 5 for node NOTCH1 and MAP4K4
looking for paths in the network with length: 6 for node NOTCH1 and MAP4K4
i_search = 3
Looking for paths with length: 0 for node NOTCH1 and MAP4K4
i_search = 3
Looking for paths with length: 1 for node NOTCH1 and MAP4K4
i_search = 3
Looking for paths with length: 2 for node NOTCH1 and MAP4K4
i_search = 3
Looking for paths with length: 3 for node NOTCH1 and MAP4K4
[['NOTCH1', 'NLK', 'MAP3K7', 'MAP4K4']]
Q9UBE8 P46531
O43318 Q9UBE8
O95819 O43318
P12931 Q05397
P12931 P12830
P12931 P19022
P12931 Q14289
P12931 P35222
P12931 O75553
P12931 Q13177
P12931 P31749
P12931 SIGNOR-PF24
P12931 P67775
P67775 P12931
P12931 P23528
P12931 P46527
P12931 P00519
P12931 P04049
P12931 SIGNOR-PF43
P17612 P12931
P12931 P61586
P12931 P06396
P12931 P00533
P12931 P60484
P35222 P46531
O75553 P46531
P46531 P04626
P46531 P37231
Q9UBE8 P46531
Q14289 Q05397
P00533 Q05397
P60484 Q05397
P12830 P35222
P19022 P35222
Q13177 P08670
P31749 P08670
SIGNOR-PF24 P08670
P06493 P08670
P17612 P08670
O95819 O43318
SIGNOR-PF41 O95835
Q13188 O95835
Q13043 O95835
SIGNOR-PH18 O95835
P06493 O95835
O95835 Q14D04
Q14D04 O95835
P35240 O95835
O60285 O95835
P17612 O95835
SIGNOR-PF41 Q9NRM7
Q13188 Q9NRM7
Q13043 Q9NRM7
SIGNOR-PH18 Q9NRM7
Q9NRM7 Q14D04
Q14D04 Q9NRM7
P35240 Q9NRM7
P17612 Q9NRM7
P31749 P35222
SIGNOR-PF24 P35222
P67775 P35222
P17612 P35222
P35222 P37231
P37231 P35222
Q13177 P00519
Q13177 P35240
P67775 P31749
P31749 SIGNOR-PF41
P31749 Q13188
P31749 Q13043
P31749 P46527
P31749 P04049
P31749 O60285
P31749 P17612
P60484 P31749
P67775 SIGNOR-PF24
SIGNOR-PF24 SIGNOR-PF41
SIGNOR-PF24 Q13188
SIGNOR-PF24 Q13043
SIGNOR-PF24 P46527
SIGNOR-PF24 P04049
SIGNOR-PF24 O60285
SIGNOR-PF24 P17612
P60484 SIGNOR-PF24
P67775 SIGNOR-PF41
P67775 Q13188
P67775 Q13043
P67775 P04049
P67775 O43318
SIGNOR-PF41 P00519
P00519 SIGNOR-PF41
P04049 SIGNOR-PF41
P35240 SIGNOR-PF41
Q13188 P00519
P00519 Q13188
P04049 Q13188
Q13188 SIGNOR-PF43
P35240 Q13188
Q13043 P00519
P00519 Q13043
P04049 Q13043
Q13043 SIGNOR-PF43
P35240 Q13043
P23528 SIGNOR-PH18
SIGNOR-PH18 SIGNOR-PF43
P61586 SIGNOR-PH18
P06396 SIGNOR-PH18
P46527 P06493
P06493 P46527
P00519 P46527
P04626 P06493
P06493 P00533
P00519 P00533
P00519 P37231
P17612 P04049
SIGNOR-PF43 Q14D04
Q14D04 SIGNOR-PF43
P35240 SIGNOR-PF43
P17612 SIGNOR-PF43
P17612 P35240
P17612 P61586
P17612 P04626
P17612 P37231
P04626 P00533
P00533 P04626
P37231 P60484
O43318 Q9UBE8
looking for paths in the network with length: 0 for node NOTCH1 and LATS1
looking for paths in the network with length: 1 for node NOTCH1 and LATS1
looking for paths in the network with length: 2 for node NOTCH1 and LATS1
looking for paths in the network with length: 3 for node NOTCH1 and LATS1
Found a path!
[['NOTCH1', 'ERBB2', 'CDK1', 'LATS1']]
looking for paths in the network with length: 0 for node NOTCH1 and LATS2
looking for paths in the network with length: 1 for node NOTCH1 and LATS2
looking for paths in the network with length: 2 for node NOTCH1 and LATS2
looking for paths in the network with length: 3 for node NOTCH1 and LATS2
looking for paths in the network with length: 4 for node NOTCH1 and LATS2
looking for paths in the network with length: 5 for node NOTCH1 and LATS2
Found a path!
[['NOTCH1', 'PPARG', 'PTEN', 'AKT1', 'PRKACA', 'LATS2'], ['NOTCH1', 'PPARG', 'PTEN', 'AKT1', 'SIGNOR-PF41', 'LATS2'], ['NOTCH1', 'PPARG', 'PTEN', 'AKT1', 'STK4', 'LATS2'], ['NOTCH1', 'PPARG', 'PTEN', 'AKT1', 'STK3', 'LATS2'], ['NOTCH1', 'PPARG', 'PTEN', 'SIGNOR-PF24', 'PRKACA', 'LATS2'], ['NOTCH1', 'PPARG', 'PTEN', 'SIGNOR-PF24', 'SIGNOR-PF41', 'LATS2'], ['NOTCH1', 'PPARG', 'PTEN', 'SIGNOR-PF24', 'STK4', 'LATS2'], ['NOTCH1', 'PPARG', 'PTEN', 'SIGNOR-PF24', 'STK3', 'LATS2'], ['NOTCH1', 'ERBB2', 'CDK1', 'LATS1', 'VEPH1', 'LATS2']]
looking for paths in the network with length: 0 for node NOTCH1 and PTK2B
looking for paths in the network with length: 1 for node NOTCH1 and PTK2B
looking for paths in the network with length: 2 for node NOTCH1 and PTK2B
looking for paths in the network with length: 3 for node NOTCH1 and PTK2B
looking for paths in the network with length: 4 for node NOTCH1 and PTK2B
looking for paths in the network with length: 5 for node NOTCH1 and PTK2B
looking for paths in the network with length: 6 for node NOTCH1 and PTK2B
Found a path!
[['NOTCH1', 'PPARG', 'PTEN', 'AKT1', 'PRKACA', 'SRC', 'PTK2B'], ['NOTCH1', 'PPARG', 'PTEN', 'SIGNOR-PF24', 'PRKACA', 'SRC', 'PTK2B']]
looking for paths in the network with length: 0 for node PTK2 and CDH1
looking for paths in the network with length: 1 for node PTK2 and CDH1
looking for paths in the network with length: 2 for node PTK2 and CDH1
looking for paths in the network with length: 3 for node PTK2 and CDH1
looking for paths in the network with length: 4 for node PTK2 and CDH1
Found a path!
[['PTK2', 'PTEN', 'PPARG', 'CTNNB1', 'CDH1']]
looking for paths in the network with length: 0 for node PTK2 and CDH2
looking for paths in the network with length: 1 for node PTK2 and CDH2
looking for paths in the network with length: 2 for node PTK2 and CDH2
looking for paths in the network with length: 3 for node PTK2 and CDH2
looking for paths in the network with length: 4 for node PTK2 and CDH2
Found a path!
[['PTK2', 'PTEN', 'PPARG', 'CTNNB1', 'CDH2']]
looking for paths in the network with length: 0 for node PTK2 and VIM
looking for paths in the network with length: 1 for node PTK2 and VIM
looking for paths in the network with length: 2 for node PTK2 and VIM
looking for paths in the network with length: 3 for node PTK2 and VIM
looking for paths in the network with length: 4 for node PTK2 and VIM
looking for paths in the network with length: 5 for node PTK2 and VIM
looking for paths in the network with length: 6 for node PTK2 and VIM
i_search = 3
Looking for paths with length: 0 for node PTK2 and VIM
i_search = 3
Looking for paths with length: 1 for node PTK2 and VIM
i_search = 3
Looking for paths with length: 2 for node PTK2 and VIM
i_search = 3
Looking for paths with length: 3 for node PTK2 and VIM
[['PTK2', 'SIGNOR-C156', 'SIGNOR-PF24', 'VIM'], ['PTK2', 'SIGNOR-C156', 'AKT1', 'VIM'], ['PTK2', 'RET', 'SIGNOR-PF24', 'VIM'], ['PTK2', 'RET', 'AKT1', 'VIM']]
Q05397 SIGNOR-C156
SIGNOR-C156 SIGNOR-PF24
SIGNOR-PF24 P08670
Q05397 SIGNOR-C156
SIGNOR-C156 P31749
P31749 P08670
Q05397 P07949
P07949 SIGNOR-PF24
SIGNOR-PF24 P08670
Q05397 P07949
P07949 P31749
P31749 P08670
P12931 Q05397
P12931 P12830
P12931 P19022
P12931 Q14289
P12931 P35222
P12931 O75553
P12931 Q13177
P12931 P31749
P12931 SIGNOR-PF24
P12931 P67775
P67775 P12931
P12931 P23528
P12931 P46527
P12931 P00519
P12931 P04049
P12931 SIGNOR-PF43
P17612 P12931
P12931 P61586
P12931 P06396
P12931 P00533
P12931 P60484
P35222 P46531
O75553 P46531
P46531 P04626
P46531 P37231
Q9UBE8 P46531
Q14289 Q05397
P00533 Q05397
P60484 Q05397
Q05397 SIGNOR-C156
Q05397 P07949
P07949 Q05397
P12830 P35222
P19022 P35222
Q13177 P08670
P31749 P08670
SIGNOR-PF24 P08670
P06493 P08670
P17612 P08670
O95819 O43318
SIGNOR-PF41 O95835
Q13188 O95835
Q13043 O95835
SIGNOR-PH18 O95835
P06493 O95835
O95835 Q14D04
Q14D04 O95835
P35240 O95835
O60285 O95835
P17612 O95835
SIGNOR-PF41 Q9NRM7
Q13188 Q9NRM7
Q13043 Q9NRM7
SIGNOR-PH18 Q9NRM7
Q9NRM7 Q14D04
Q14D04 Q9NRM7
P35240 Q9NRM7
P17612 Q9NRM7
P31749 P35222
SIGNOR-PF24 P35222
P67775 P35222
P17612 P35222
P35222 P37231
P37231 P35222
Q13177 P00519
Q13177 P35240
P67775 P31749
P31749 SIGNOR-PF41
P31749 Q13188
P31749 Q13043
P31749 P46527
P31749 P04049
P31749 O60285
P31749 P17612
P60484 P31749
SIGNOR-C156 P31749
P07949 P31749
P67775 SIGNOR-PF24
SIGNOR-PF24 SIGNOR-PF41
SIGNOR-PF24 Q13188
SIGNOR-PF24 Q13043
SIGNOR-PF24 P46527
SIGNOR-PF24 P04049
SIGNOR-PF24 O60285
SIGNOR-PF24 P17612
P60484 SIGNOR-PF24
SIGNOR-C156 SIGNOR-PF24
P07949 SIGNOR-PF24
P67775 SIGNOR-PF41
P67775 Q13188
P67775 Q13043
P67775 P04049
P67775 O43318
SIGNOR-PF41 P00519
P00519 SIGNOR-PF41
P04049 SIGNOR-PF41
P35240 SIGNOR-PF41
Q13188 P00519
P00519 Q13188
P04049 Q13188
Q13188 SIGNOR-PF43
P35240 Q13188
Q13043 P00519
P00519 Q13043
P04049 Q13043
Q13043 SIGNOR-PF43
P35240 Q13043
P23528 SIGNOR-PH18
SIGNOR-PH18 SIGNOR-PF43
P61586 SIGNOR-PH18
P06396 SIGNOR-PH18
P46527 P06493
P06493 P46527
P00519 P46527
P04626 P06493
P06493 P00533
P00519 P00533
P00519 P37231
P17612 P04049
SIGNOR-PF43 Q14D04
Q14D04 SIGNOR-PF43
P35240 SIGNOR-PF43
P17612 SIGNOR-PF43
P17612 P35240
P17612 P61586
P17612 P04626
P17612 P37231
P17612 P07949
P04626 P00533
P00533 P04626
P00533 SIGNOR-C156
P37231 P60484
P60484 SIGNOR-C156
O43318 Q9UBE8
looking for paths in the network with length: 0 for node PTK2 and MAP4K4
looking for paths in the network with length: 1 for node PTK2 and MAP4K4
looking for paths in the network with length: 2 for node PTK2 and MAP4K4
looking for paths in the network with length: 3 for node PTK2 and MAP4K4
looking for paths in the network with length: 4 for node PTK2 and MAP4K4
looking for paths in the network with length: 5 for node PTK2 and MAP4K4
looking for paths in the network with length: 6 for node PTK2 and MAP4K4
Found a path!
[['PTK2', 'PTEN', 'PPARG', 'NOTCH1', 'NLK', 'MAP3K7', 'MAP4K4'], ['PTK2', 'EGFR', 'ERBB2', 'NOTCH1', 'NLK', 'MAP3K7', 'MAP4K4']]
looking for paths in the network with length: 0 for node PTK2 and LATS1
looking for paths in the network with length: 1 for node PTK2 and LATS1
looking for paths in the network with length: 2 for node PTK2 and LATS1
looking for paths in the network with length: 3 for node PTK2 and LATS1
looking for paths in the network with length: 4 for node PTK2 and LATS1
Found a path!
[['PTK2', 'SIGNOR-C156', 'AKT1', 'PRKACA', 'LATS1'], ['PTK2', 'SIGNOR-C156', 'AKT1', 'NUAK1', 'LATS1'], ['PTK2', 'SIGNOR-C156', 'AKT1', 'SIGNOR-PF41', 'LATS1'], ['PTK2', 'SIGNOR-C156', 'AKT1', 'STK4', 'LATS1'], ['PTK2', 'SIGNOR-C156', 'AKT1', 'STK3', 'LATS1'], ['PTK2', 'SIGNOR-C156', 'SIGNOR-PF24', 'PRKACA', 'LATS1'], ['PTK2', 'SIGNOR-C156', 'SIGNOR-PF24', 'NUAK1', 'LATS1'], ['PTK2', 'SIGNOR-C156', 'SIGNOR-PF24', 'SIGNOR-PF41', 'LATS1'], ['PTK2', 'SIGNOR-C156', 'SIGNOR-PF24', 'STK4', 'LATS1'], ['PTK2', 'SIGNOR-C156', 'SIGNOR-PF24', 'STK3', 'LATS1'], ['PTK2', 'RET', 'AKT1', 'PRKACA', 'LATS1'], ['PTK2', 'RET', 'AKT1', 'NUAK1', 'LATS1'], ['PTK2', 'RET', 'AKT1', 'SIGNOR-PF41', 'LATS1'], ['PTK2', 'RET', 'AKT1', 'STK4', 'LATS1'], ['PTK2', 'RET', 'AKT1', 'STK3', 'LATS1'], ['PTK2', 'RET', 'SIGNOR-PF24', 'PRKACA', 'LATS1'], ['PTK2', 'RET', 'SIGNOR-PF24', 'NUAK1', 'LATS1'], ['PTK2', 'RET', 'SIGNOR-PF24', 'SIGNOR-PF41', 'LATS1'], ['PTK2', 'RET', 'SIGNOR-PF24', 'STK4', 'LATS1'], ['PTK2', 'RET', 'SIGNOR-PF24', 'STK3', 'LATS1']]
looking for paths in the network with length: 0 for node PTK2 and LATS2
looking for paths in the network with length: 1 for node PTK2 and LATS2
looking for paths in the network with length: 2 for node PTK2 and LATS2
looking for paths in the network with length: 3 for node PTK2 and LATS2
looking for paths in the network with length: 4 for node PTK2 and LATS2
Found a path!
[['PTK2', 'SIGNOR-C156', 'AKT1', 'PRKACA', 'LATS2'], ['PTK2', 'SIGNOR-C156', 'AKT1', 'SIGNOR-PF41', 'LATS2'], ['PTK2', 'SIGNOR-C156', 'AKT1', 'STK4', 'LATS2'], ['PTK2', 'SIGNOR-C156', 'AKT1', 'STK3', 'LATS2'], ['PTK2', 'SIGNOR-C156', 'SIGNOR-PF24', 'PRKACA', 'LATS2'], ['PTK2', 'SIGNOR-C156', 'SIGNOR-PF24', 'SIGNOR-PF41', 'LATS2'], ['PTK2', 'SIGNOR-C156', 'SIGNOR-PF24', 'STK4', 'LATS2'], ['PTK2', 'SIGNOR-C156', 'SIGNOR-PF24', 'STK3', 'LATS2'], ['PTK2', 'RET', 'AKT1', 'PRKACA', 'LATS2'], ['PTK2', 'RET', 'AKT1', 'SIGNOR-PF41', 'LATS2'], ['PTK2', 'RET', 'AKT1', 'STK4', 'LATS2'], ['PTK2', 'RET', 'AKT1', 'STK3', 'LATS2'], ['PTK2', 'RET', 'SIGNOR-PF24', 'PRKACA', 'LATS2'], ['PTK2', 'RET', 'SIGNOR-PF24', 'SIGNOR-PF41', 'LATS2'], ['PTK2', 'RET', 'SIGNOR-PF24', 'STK4', 'LATS2'], ['PTK2', 'RET', 'SIGNOR-PF24', 'STK3', 'LATS2']]
looking for paths in the network with length: 0 for node PTK2 and PTK2B
looking for paths in the network with length: 1 for node PTK2 and PTK2B
Found a path!
[['PTK2', 'PTK2B']]
looking for paths in the network with length: 0 for node CDH1 and CDH2
looking for paths in the network with length: 1 for node CDH1 and CDH2
looking for paths in the network with length: 2 for node CDH1 and CDH2
looking for paths in the network with length: 3 for node CDH1 and CDH2
looking for paths in the network with length: 4 for node CDH1 and CDH2
looking for paths in the network with length: 5 for node CDH1 and CDH2
looking for paths in the network with length: 6 for node CDH1 and CDH2
i_search = 3
Looking for paths with length: 0 for node CDH1 and CDH2
i_search = 3
Looking for paths with length: 1 for node CDH1 and CDH2
i_search = 3
Looking for paths with length: 2 for node CDH1 and CDH2
i_search = 3
Looking for paths with length: 3 for node CDH1 and CDH2
[['CDH1', 'SIGNOR-PF72', 'CTNNB1', 'CDH2']]
P12830 SIGNOR-PF72
SIGNOR-PF72 P35222
P19022 P35222
P12931 Q05397
P12931 P12830
P12931 P19022
P12931 Q14289
P12931 P35222
P12931 O75553
P12931 Q13177
P12931 P31749
P12931 SIGNOR-PF24
P12931 P67775
P67775 P12931
P12931 P23528
P12931 P46527
P12931 P00519
P12931 P04049
P12931 SIGNOR-PF43
P17612 P12931
P12931 P61586
P12931 P06396
P12931 P00533
P12931 P60484
P35222 P46531
O75553 P46531
P46531 P04626
P46531 P37231
Q9UBE8 P46531
Q14289 Q05397
P00533 Q05397
P60484 Q05397
Q05397 SIGNOR-C156
Q05397 P07949
P07949 Q05397
P12830 P35222
P12830 SIGNOR-PF72
SIGNOR-PF72 P12830
P19022 P35222
Q13177 P08670
P31749 P08670
SIGNOR-PF24 P08670
P06493 P08670
P17612 P08670
O95819 O43318
SIGNOR-PF41 O95835
Q13188 O95835
Q13043 O95835
SIGNOR-PH18 O95835
P06493 O95835
O95835 Q14D04
Q14D04 O95835
P35240 O95835
O60285 O95835
P17612 O95835
SIGNOR-PF41 Q9NRM7
Q13188 Q9NRM7
Q13043 Q9NRM7
SIGNOR-PH18 Q9NRM7
Q9NRM7 Q14D04
Q14D04 Q9NRM7
P35240 Q9NRM7
P17612 Q9NRM7
P31749 P35222
SIGNOR-PF24 P35222
P67775 P35222
P17612 P35222
P35222 P37231
P37231 P35222
P35222 SIGNOR-PF72
SIGNOR-PF72 P35222
Q13177 P00519
Q13177 P35240
P67775 P31749
P31749 SIGNOR-PF41
P31749 Q13188
P31749 Q13043
P31749 P46527
P31749 P04049
P31749 O60285
P31749 P17612
P60484 P31749
SIGNOR-C156 P31749
P07949 P31749
P67775 SIGNOR-PF24
SIGNOR-PF24 SIGNOR-PF41
SIGNOR-PF24 Q13188
SIGNOR-PF24 Q13043
SIGNOR-PF24 P46527
SIGNOR-PF24 P04049
SIGNOR-PF24 O60285
SIGNOR-PF24 P17612
P60484 SIGNOR-PF24
SIGNOR-C156 SIGNOR-PF24
P07949 SIGNOR-PF24
P67775 SIGNOR-PF41
P67775 Q13188
P67775 Q13043
P67775 P04049
P67775 O43318
SIGNOR-PF41 P00519
P00519 SIGNOR-PF41
P04049 SIGNOR-PF41
P35240 SIGNOR-PF41
Q13188 P00519
P00519 Q13188
P04049 Q13188
Q13188 SIGNOR-PF43
P35240 Q13188
Q13043 P00519
P00519 Q13043
P04049 Q13043
Q13043 SIGNOR-PF43
P35240 Q13043
P23528 SIGNOR-PH18
SIGNOR-PH18 SIGNOR-PF43
P61586 SIGNOR-PH18
P06396 SIGNOR-PH18
SIGNOR-PF72 SIGNOR-PH18
P46527 P06493
P06493 P46527
P00519 P46527
P04626 P06493
P06493 P00533
P00519 P00533
P00519 P37231
P17612 P04049
SIGNOR-PF43 Q14D04
Q14D04 SIGNOR-PF43
P35240 SIGNOR-PF43
P17612 SIGNOR-PF43
P17612 P35240
P17612 P61586
P17612 P04626
P17612 P37231
P17612 P07949
P04626 P00533
P00533 P04626
P00533 SIGNOR-C156
P37231 P60484
P60484 SIGNOR-C156
O43318 Q9UBE8
looking for paths in the network with length: 0 for node CDH1 and VIM
looking for paths in the network with length: 1 for node CDH1 and VIM
looking for paths in the network with length: 2 for node CDH1 and VIM
looking for paths in the network with length: 3 for node CDH1 and VIM
looking for paths in the network with length: 4 for node CDH1 and VIM
looking for paths in the network with length: 5 for node CDH1 and VIM
Found a path!
[['CDH1', 'CTNNB1', 'PPARG', 'PTEN', 'AKT1', 'VIM'], ['CDH1', 'CTNNB1', 'PPARG', 'PTEN', 'SIGNOR-PF24', 'VIM'], ['CDH1', 'CTNNB1', 'NOTCH1', 'ERBB2', 'CDK1', 'VIM']]
looking for paths in the network with length: 0 for node CDH1 and MAP4K4
looking for paths in the network with length: 1 for node CDH1 and MAP4K4
looking for paths in the network with length: 2 for node CDH1 and MAP4K4
looking for paths in the network with length: 3 for node CDH1 and MAP4K4
looking for paths in the network with length: 4 for node CDH1 and MAP4K4
looking for paths in the network with length: 5 for node CDH1 and MAP4K4
looking for paths in the network with length: 6 for node CDH1 and MAP4K4
i_search = 3
Looking for paths with length: 0 for node CDH1 and MAP4K4
i_search = 3
Looking for paths with length: 1 for node CDH1 and MAP4K4
i_search = 3
Looking for paths with length: 2 for node CDH1 and MAP4K4
i_search = 3
Looking for paths with length: 3 for node CDH1 and MAP4K4
looking for paths in the network with length: 0 for node CDH1 and LATS1
looking for paths in the network with length: 1 for node CDH1 and LATS1
looking for paths in the network with length: 2 for node CDH1 and LATS1
looking for paths in the network with length: 3 for node CDH1 and LATS1
Found a path!
[['CDH1', 'SIGNOR-PF72', 'SIGNOR-PH18', 'LATS1']]
looking for paths in the network with length: 0 for node CDH1 and LATS2
looking for paths in the network with length: 1 for node CDH1 and LATS2
looking for paths in the network with length: 2 for node CDH1 and LATS2
looking for paths in the network with length: 3 for node CDH1 and LATS2
Found a path!
[['CDH1', 'SIGNOR-PF72', 'SIGNOR-PH18', 'LATS2']]
looking for paths in the network with length: 0 for node CDH1 and PTK2B
looking for paths in the network with length: 1 for node CDH1 and PTK2B
looking for paths in the network with length: 2 for node CDH1 and PTK2B
looking for paths in the network with length: 3 for node CDH1 and PTK2B
looking for paths in the network with length: 4 for node CDH1 and PTK2B
looking for paths in the network with length: 5 for node CDH1 and PTK2B
looking for paths in the network with length: 6 for node CDH1 and PTK2B
Found a path!
[['CDH1', 'SRC', 'PRKACA', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['CDH1', 'SRC', 'PRKACA', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['CDH1', 'SRC', 'PRKACA', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['CDH1', 'SRC', 'PRKACA', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B'], ['CDH1', 'SIGNOR-PF72', 'CTNNB1', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['CDH1', 'SIGNOR-PF72', 'CTNNB1', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['CDH1', 'SIGNOR-PF72', 'CTNNB1', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['CDH1', 'SIGNOR-PF72', 'CTNNB1', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B']]
looking for paths in the network with length: 0 for node CDH2 and VIM
looking for paths in the network with length: 1 for node CDH2 and VIM
looking for paths in the network with length: 2 for node CDH2 and VIM
looking for paths in the network with length: 3 for node CDH2 and VIM
looking for paths in the network with length: 4 for node CDH2 and VIM
looking for paths in the network with length: 5 for node CDH2 and VIM
Found a path!
[['CDH2', 'CTNNB1', 'PPARG', 'PTEN', 'AKT1', 'VIM'], ['CDH2', 'CTNNB1', 'PPARG', 'PTEN', 'SIGNOR-PF24', 'VIM'], ['CDH2', 'CTNNB1', 'NOTCH1', 'ERBB2', 'CDK1', 'VIM']]
looking for paths in the network with length: 0 for node CDH2 and MAP4K4
looking for paths in the network with length: 1 for node CDH2 and MAP4K4
looking for paths in the network with length: 2 for node CDH2 and MAP4K4
looking for paths in the network with length: 3 for node CDH2 and MAP4K4
looking for paths in the network with length: 4 for node CDH2 and MAP4K4
looking for paths in the network with length: 5 for node CDH2 and MAP4K4
looking for paths in the network with length: 6 for node CDH2 and MAP4K4
i_search = 3
Looking for paths with length: 0 for node CDH2 and MAP4K4
i_search = 3
Looking for paths with length: 1 for node CDH2 and MAP4K4
i_search = 3
Looking for paths with length: 2 for node CDH2 and MAP4K4
i_search = 3
Looking for paths with length: 3 for node CDH2 and MAP4K4
looking for paths in the network with length: 0 for node CDH2 and LATS1
looking for paths in the network with length: 1 for node CDH2 and LATS1
looking for paths in the network with length: 2 for node CDH2 and LATS1
looking for paths in the network with length: 3 for node CDH2 and LATS1
looking for paths in the network with length: 4 for node CDH2 and LATS1
Found a path!
[['CDH2', 'CTNNB1', 'SIGNOR-PF72', 'SIGNOR-PH18', 'LATS1']]
looking for paths in the network with length: 0 for node CDH2 and LATS2
looking for paths in the network with length: 1 for node CDH2 and LATS2
looking for paths in the network with length: 2 for node CDH2 and LATS2
looking for paths in the network with length: 3 for node CDH2 and LATS2
looking for paths in the network with length: 4 for node CDH2 and LATS2
Found a path!
[['CDH2', 'CTNNB1', 'SIGNOR-PF72', 'SIGNOR-PH18', 'LATS2']]
looking for paths in the network with length: 0 for node CDH2 and PTK2B
looking for paths in the network with length: 1 for node CDH2 and PTK2B
looking for paths in the network with length: 2 for node CDH2 and PTK2B
looking for paths in the network with length: 3 for node CDH2 and PTK2B
looking for paths in the network with length: 4 for node CDH2 and PTK2B
looking for paths in the network with length: 5 for node CDH2 and PTK2B
looking for paths in the network with length: 6 for node CDH2 and PTK2B
Found a path!
[['CDH2', 'SRC', 'PRKACA', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['CDH2', 'SRC', 'PRKACA', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['CDH2', 'SRC', 'PRKACA', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['CDH2', 'SRC', 'PRKACA', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B']]
looking for paths in the network with length: 0 for node VIM and MAP4K4
looking for paths in the network with length: 1 for node VIM and MAP4K4
looking for paths in the network with length: 2 for node VIM and MAP4K4
looking for paths in the network with length: 3 for node VIM and MAP4K4
looking for paths in the network with length: 4 for node VIM and MAP4K4
looking for paths in the network with length: 5 for node VIM and MAP4K4
looking for paths in the network with length: 6 for node VIM and MAP4K4
Found a path!
[['VIM', 'CDK1', 'ERBB2', 'NOTCH1', 'NLK', 'MAP3K7', 'MAP4K4']]
looking for paths in the network with length: 0 for node VIM and LATS1
looking for paths in the network with length: 1 for node VIM and LATS1
looking for paths in the network with length: 2 for node VIM and LATS1
looking for paths in the network with length: 3 for node VIM and LATS1
looking for paths in the network with length: 4 for node VIM and LATS1
looking for paths in the network with length: 5 for node VIM and LATS1
looking for paths in the network with length: 6 for node VIM and LATS1
i_search = 3
Looking for paths with length: 0 for node VIM and LATS1
i_search = 3
Looking for paths with length: 1 for node VIM and LATS1
i_search = 3
Looking for paths with length: 2 for node VIM and LATS1
i_search = 3
Looking for paths with length: 3 for node VIM and LATS1
looking for paths in the network with length: 0 for node VIM and LATS2
looking for paths in the network with length: 1 for node VIM and LATS2
looking for paths in the network with length: 2 for node VIM and LATS2
looking for paths in the network with length: 3 for node VIM and LATS2
looking for paths in the network with length: 4 for node VIM and LATS2
looking for paths in the network with length: 5 for node VIM and LATS2
looking for paths in the network with length: 6 for node VIM and LATS2
i_search = 3
Looking for paths with length: 0 for node VIM and LATS2
i_search = 3
Looking for paths with length: 1 for node VIM and LATS2
i_search = 3
Looking for paths with length: 2 for node VIM and LATS2
i_search = 3
Looking for paths with length: 3 for node VIM and LATS2
looking for paths in the network with length: 0 for node VIM and PTK2B
looking for paths in the network with length: 1 for node VIM and PTK2B
looking for paths in the network with length: 2 for node VIM and PTK2B
looking for paths in the network with length: 3 for node VIM and PTK2B
looking for paths in the network with length: 4 for node VIM and PTK2B
Found a path!
[['VIM', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['VIM', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['VIM', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['VIM', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B']]
looking for paths in the network with length: 0 for node MAP4K4 and LATS1
looking for paths in the network with length: 1 for node MAP4K4 and LATS1
looking for paths in the network with length: 2 for node MAP4K4 and LATS1
looking for paths in the network with length: 3 for node MAP4K4 and LATS1
looking for paths in the network with length: 4 for node MAP4K4 and LATS1
looking for paths in the network with length: 5 for node MAP4K4 and LATS1
looking for paths in the network with length: 6 for node MAP4K4 and LATS1
Found a path!
[['MAP4K4', 'MAP3K7', 'NLK', 'NOTCH1', 'ERBB2', 'CDK1', 'LATS1']]
looking for paths in the network with length: 0 for node MAP4K4 and LATS2
looking for paths in the network with length: 1 for node MAP4K4 and LATS2
looking for paths in the network with length: 2 for node MAP4K4 and LATS2
looking for paths in the network with length: 3 for node MAP4K4 and LATS2
looking for paths in the network with length: 4 for node MAP4K4 and LATS2
looking for paths in the network with length: 5 for node MAP4K4 and LATS2
looking for paths in the network with length: 6 for node MAP4K4 and LATS2
i_search = 3
Looking for paths with length: 0 for node MAP4K4 and LATS2
i_search = 3
Looking for paths with length: 1 for node MAP4K4 and LATS2
i_search = 3
Looking for paths with length: 2 for node MAP4K4 and LATS2
i_search = 3
Looking for paths with length: 3 for node MAP4K4 and LATS2
looking for paths in the network with length: 0 for node MAP4K4 and PTK2B
looking for paths in the network with length: 1 for node MAP4K4 and PTK2B
looking for paths in the network with length: 2 for node MAP4K4 and PTK2B
looking for paths in the network with length: 3 for node MAP4K4 and PTK2B
looking for paths in the network with length: 4 for node MAP4K4 and PTK2B
looking for paths in the network with length: 5 for node MAP4K4 and PTK2B
looking for paths in the network with length: 6 for node MAP4K4 and PTK2B
i_search = 3
Looking for paths with length: 0 for node MAP4K4 and PTK2B
i_search = 3
Looking for paths with length: 1 for node MAP4K4 and PTK2B
i_search = 3
Looking for paths with length: 2 for node MAP4K4 and PTK2B
i_search = 3
Looking for paths with length: 3 for node MAP4K4 and PTK2B
looking for paths in the network with length: 0 for node LATS1 and LATS2
looking for paths in the network with length: 1 for node LATS1 and LATS2
looking for paths in the network with length: 2 for node LATS1 and LATS2
Found a path!
[['LATS1', 'VEPH1', 'LATS2'], ['LATS1', 'VEPH1', 'LATS2']]
looking for paths in the network with length: 0 for node LATS1 and PTK2B
looking for paths in the network with length: 1 for node LATS1 and PTK2B
looking for paths in the network with length: 2 for node LATS1 and PTK2B
looking for paths in the network with length: 3 for node LATS1 and PTK2B
looking for paths in the network with length: 4 for node LATS1 and PTK2B
looking for paths in the network with length: 5 for node LATS1 and PTK2B
Found a path!
[['LATS1', 'PRKACA', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS1', 'PRKACA', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['LATS1', 'PRKACA', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS1', 'PRKACA', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B'], ['LATS1', 'NUAK1', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS1', 'NUAK1', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['LATS1', 'NUAK1', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS1', 'NUAK1', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B'], ['LATS1', 'SIGNOR-PF41', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS1', 'SIGNOR-PF41', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['LATS1', 'SIGNOR-PF41', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS1', 'SIGNOR-PF41', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B'], ['LATS1', 'STK4', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS1', 'STK4', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['LATS1', 'STK4', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS1', 'STK4', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B'], ['LATS1', 'STK3', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS1', 'STK3', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['LATS1', 'STK3', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS1', 'STK3', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B']]
looking for paths in the network with length: 0 for node LATS2 and PTK2B
looking for paths in the network with length: 1 for node LATS2 and PTK2B
looking for paths in the network with length: 2 for node LATS2 and PTK2B
looking for paths in the network with length: 3 for node LATS2 and PTK2B
looking for paths in the network with length: 4 for node LATS2 and PTK2B
looking for paths in the network with length: 5 for node LATS2 and PTK2B
Found a path!
[['LATS2', 'PRKACA', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS2', 'PRKACA', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['LATS2', 'PRKACA', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS2', 'PRKACA', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B'], ['LATS2', 'SIGNOR-PF41', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS2', 'SIGNOR-PF41', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['LATS2', 'SIGNOR-PF41', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS2', 'SIGNOR-PF41', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B'], ['LATS2', 'STK4', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS2', 'STK4', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['LATS2', 'STK4', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS2', 'STK4', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B'], ['LATS2', 'STK3', 'AKT1', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS2', 'STK3', 'AKT1', 'RET', 'PTK2', 'PTK2B'], ['LATS2', 'STK3', 'SIGNOR-PF24', 'SIGNOR-C156', 'PTK2', 'PTK2B'], ['LATS2', 'STK3', 'SIGNOR-PF24', 'RET', 'PTK2', 'PTK2B']]
CPU times: user 1min 3s, sys: 84.4 ms, total: 1min 3s
Wall time: 1min 3s
[13]:
#Visualize network
visualizer1 = NetworkVisualizer(new_net1, color_by='effect')
visualizer1.render()
[ ]:
from neko._outputs.exports import Exports
[ ]:
export = Exports(new_net1)
[ ]:
export.export_bnet()
export.export_sif()