Exploring Network History in NeKo¶
This notebook demonstrates the new history facilities in NeKo. You will learn how to:
- capture network states automatically while you enrich a network
- inspect branches and metadata associated with each state
- visualise the history graph as both a
networkxobject and an embedded SVG - control the history recorder with context managers and global toggles
- prune older history entries using
set_max_history
In [1]:
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import pandas as pd
from IPython.display import display, HTML
from neko.core.network import Network
import pandas as pd
from IPython.display import display, HTML
from neko.core.network import Network
1. Create a network using the Omnipath database¶
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net = Network(initial_nodes=["SRC", "CDH1", "TP53"], resources="omnipath")
net.list_states()
net = Network(initial_nodes=["SRC", "CDH1", "TP53"], resources="omnipath")
net.list_states()
Out[2]:
[{'id': 0, 'metadata': {'label': 'initial'}}]
2. Automatic history capture¶
Every mutating API call creates a new state with metadata describing the operation.
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net.add_node("TP63")
net.add_node("FAK")
net.list_states()
net.add_node("TP63")
net.add_node("FAK")
net.list_states()
Out[3]:
[{'id': 0, 'metadata': {'label': 'initial'}},
{'id': 1, 'metadata': {'method': 'add_node', 'args': ['TP63'], 'kwargs': {}}},
{'id': 2, 'metadata': {'method': 'add_node', 'args': ['PTK2'], 'kwargs': {}}}]
We can compare branches or move around the history using checkout, undo, and redo.
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current = net.current_state_id
print("Current state ID:", current)
current = net.current_state_id
print("Current state ID:", current)
Current state ID: 2
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net.undo()
net.undo()
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net.nodes
net.nodes
Out[6]:
| Genesymbol | Uniprot | Type | |
|---|---|---|---|
| 0 | SRC | P12931 | NaN |
| 1 | CDH1 | P12830 | NaN |
| 2 | TP53 | P04637 | NaN |
| 3 | TP63 | Q9H3D4 | NaN |
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net.redo()
net.nodes
net.redo()
net.nodes
Out[7]:
| Genesymbol | Uniprot | Type | |
|---|---|---|---|
| 0 | SRC | P12931 | NaN |
| 1 | CDH1 | P12830 | NaN |
| 2 | TP53 | P04637 | NaN |
| 3 | TP63 | Q9H3D4 | NaN |
| 4 | PTK2 | Q05397 | NaN |
3. Visualising the history graph¶
history_graph() returns a networkx object, while history_html() embeds a Graphviz SVG.
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history_nx = net.history_graph()
list(history_nx.edges())
history_nx = net.history_graph()
list(history_nx.edges())
Out[8]:
[(0, 1), (1, 2)]
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HTML(net.history_html())
HTML(net.history_html())
Out[9]:
4. Working with branches¶
We can revert to an earlier state, explore an alternative enrichment strategy, and compare the resulting states.
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root_state = net.root_state_id
net.checkout(root_state)
net.add_node("P01112")
branch_state = net.current_state_id
diff = net.compare_states(current, branch_state)
diff
root_state = net.root_state_id
net.checkout(root_state)
net.add_node("P01112")
branch_state = net.current_state_id
diff = net.compare_states(current, branch_state)
diff
Out[25]:
{'added_nodes': ['P01112'],
'removed_nodes': ['Q05397', 'Q9H3D4'],
'added_edges': [],
'removed_edges': [],
'added_provenance': [],
'removed_provenance': []}
5. Suspension and toggles¶
Use suspend_history() or set_history_tracking(False) to batch changes without recording intermediate states.
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with net.suspend_history():
net.add_node("Q9Y243") # already present, but no state recorded
net.list_states()[-1]
with net.suspend_history():
net.add_node("Q9Y243") # already present, but no state recorded
net.list_states()[-1]
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net.set_history_tracking(False)
net.add_node("Q15796")
net.set_history_tracking(True)
net.list_states()
net.set_history_tracking(False)
net.add_node("Q15796")
net.set_history_tracking(True)
net.list_states()
Out[27]:
[{'id': 0, 'metadata': {'label': 'initial'}},
{'id': 1,
'metadata': {'method': 'add_node', 'args': ["'TP63'"], 'kwargs': {}}},
{'id': 2,
'metadata': {'method': 'add_node', 'args': ["'FAK'"], 'kwargs': {}}},
{'id': 3,
'metadata': {'method': 'add_node', 'args': ["'P01112'"], 'kwargs': {}}}]
6. Pruning history¶
set_max_history() limits the number of stored states while preserving the root and the latest state.
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net.set_max_history(4)
for node in ["Q9Y6K9", "P17302"]:
if node not in net.nodes["Genesymbol"].tolist():
net.add_node(node)
net.list_states()
net.set_max_history(4)
for node in ["Q9Y6K9", "P17302"]:
if node not in net.nodes["Genesymbol"].tolist():
net.add_node(node)
net.list_states()
Out[28]:
[{'id': 0, 'metadata': {'label': 'initial'}},
{'id': 3,
'metadata': {'method': 'add_node', 'args': ["'P01112'"], 'kwargs': {}}},
{'id': 4,
'metadata': {'method': 'add_node', 'args': ["'Q9Y6K9'"], 'kwargs': {}}},
{'id': 5,
'metadata': {'method': 'add_node', 'args': ["'P17302'"], 'kwargs': {}}}]
When the number of stored states exceeds the limit, older leaf states are pruned automatically. The root and current state remain intact.
This concludes the walkthrough of the history API. Experiment by combining these features with your favourite enrichment strategies to analyse multiple hypotheses side by side.
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net = Network(initial_nodes=["SRC", "CDH1", "TP53"], resources="omnipath")
net = Network(initial_nodes=["SRC", "CDH1", "TP53"], resources="omnipath")
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net.complete_connection(maxlen=2, path_policy="one_shortest", reuse_policy="discovered_paths", only_signed=True, consensus=True)
net.complete_connection(maxlen=2, path_policy="one_shortest", reuse_policy="discovered_paths", only_signed=True, consensus=True)
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net.edges
net.edges
Out[12]:
| source | target | Type | Effect | References | Provenance | |
|---|---|---|---|---|---|---|
| 0 | P12830 | P12931 | None | stimulation | ACSN:16039586;ACSN:16099633;ACSN:17143292;ACSN... | None |
| 1 | P12931 | P07949 | None | stimulation | BioGRID:10070972;HPRD:10070972;KEA:11713247;KE... | None |
| 2 | P07949 | P12830 | None | stimulation | NaN | None |
| 3 | P04637 | P14210 | None | stimulation | SPIKE:18431400;SPIKE_LC:18431400; SPIKE:184314... | None |
| 4 | P14210 | P12931 | None | stimulation | ProtMapper:23524339; ProtMapper:23524339 | None |
| 5 | P12931 | Q14289 | None | stimulation | Adhesome:10329689;Adhesome:10521452;Adhesome:1... | None |
| 6 | Q14289 | P04637 | None | stimulation | NaN | None |
| 7 | P04637 | Q15910 | None | inhibition | NaN | None |
| 8 | Q15910 | P12830 | None | inhibition | ACSN:11309385;ACSN:12508111;ACSN:14673164;ACSN... | None |
| 9 | P12830 | P63000 | None | stimulation | NaN | None |
| 10 | P63000 | P04637 | None | stimulation | NaN | None |
| 11 | P12931 | P63000 | None | stimulation | ProtMapper:21798346;ProtMapper:22163037;ProtMa... | None |
| 12 | P12830 | P14210 | None | inhibition | NaN | None |
| 13 | P63000 | P12830 | None | inhibition | NaN | None |
| 14 | P04637 | P63000 | None | inhibition | NaN | None |
| 15 | P14210 | P63000 | None | stimulation | NaN | None |
| 16 | Q14289 | P63000 | None | stimulation | Adhesome:10592173 | None |
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net.undo()
net.undo()
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net.edges
net.edges
Out[14]:
| source | target | Type | Effect | References | Provenance |
|---|
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net.connect_network_radially(max_len=1, only_signed=True, consensus=True)
net.connect_network_radially(max_len=1, only_signed=True, consensus=True)
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net.edges
net.edges
Out[16]:
| source | target | Type | Effect | References | Provenance | |
|---|---|---|---|---|---|---|
| 13 | P12830 | P12931 | None | stimulation | ACSN:16039586;ACSN:16099633;ACSN:17143292;ACSN... | None |
| 14 | P12830 | P01133 | None | inhibition | NaN | None |
| 15 | P12830 | P62834 | None | stimulation | NaN | None |
| 20 | P12830 | P14210 | None | inhibition | NaN | None |
| 23 | P12830 | P63000 | None | stimulation | NaN | None |
| ... | ... | ... | ... | ... | ... | ... |
| 915 | P08151 | P04637 | None | inhibition | NaN | None |
| 932 | P61978 | P04637 | None | stimulation | InnateDB:23092970;SPIKE:16360036;SPIKE:1847200... | None |
| 957 | P98170 | P04637 | None | stimulation | NaN | None |
| 962 | P09038 | P04637 | None | inhibition | NaN | None |
| 963 | Q07817 | P04637 | None | inhibition | BioGRID:24474649;DIP:24814347;HPRD:12667443;HP... | None |
120 rows × 6 columns
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net.list_states()
net.list_states()
Out[17]:
[{'id': 0, 'metadata': {'label': 'initial'}},
{'id': 1,
'metadata': {'method': 'complete_connection',
'args': [],
'kwargs': {'maxlen': '2',
'algorithm': 'bfs',
'only_signed': 'True',
'consensus': 'True'}}},
{'id': 2,
'metadata': {'method': 'connect_network_radially',
'args': [],
'kwargs': {'max_len': '1', 'only_signed': 'True', 'consensus': 'True'}}}]
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history_nx = net.history_graph()
list(history_nx.edges())
history_nx = net.history_graph()
list(history_nx.edges())
Out[18]:
[(0, 1), (0, 2)]
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HTML(net.history_html())
HTML(net.history_html())
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net.compare_states(1, 2)
net.compare_states(1, 2)
Out[20]:
{'added_nodes': ['GJA1',
'HIPK2',
'SNAI2',
'ITGB6',
'ITGB8',
'PTP4A1',
'PRKD1',
'ZYX',
'MAPK11',
'EPHB1',
'PIK3R3',
'HMGB1',
'EGF',
'RAP1A',
'FGF2',
'PPP2CA',
'DEK',
'HSPA1B',
'NFKB1',
'AR',
'MAPK1',
'CDC42',
'GDNF',
'FOS',
'HNRNPK',
'TLN1',
'PDGFD',
'NUMB',
'GRK2',
'BCL2L1',
'WRN',
'PDGFRB',
'CTNND1',
'MAPK14',
'GFRA1',
'PAK4',
'GLI1',
'BCL6',
'CTNNA1',
'ITGB5',
'DAPK1',
'ITGB4',
'MET',
'NR3C1',
'VAV1',
'XIAP',
'MAPK3',
'PRKCD',
'HSPA1A',
'S100A4'],
'removed_nodes': [],
'added_edges': [('MAPK11',
'TP53',
None,
'stimulation',
'ACSN:11274345;ACSN:15140942;ACSN:15187187;ACSN:16393692;ACSN:19436832;ACSN:20506250;ACSN:21614932;ProtMapper:10212189;SIGNOR:17254968;SPIKE_LC:17145710',
None),
('TP53', 'DEK', None, 'inhibition', nan, None),
('MAPK1',
'TP53',
None,
'stimulation',
'BioGRID:15867353;HPRD-phos:11409876;HPRD-phos:15116093;HPRD:11409876;HPRD:12091386;HPRD:15116093;InnateDB:10958792;KEA:10446957;KEA:10673501;KEA:11409876;KEA:11551930;KEA:11709713;KEA:11875057;KEA:12091386;KEA:14965474;KEA:15116093;KEA:9765199;Lit-BM-17:10958792;Lit-BM-17:21147777;Lit-BM-17:21675959;Lit-BM-17:23443559;Lit-BM-17:25241761;ProtMapper:11409876;ProtMapper:15116093;iPTMnet:10781582;iPTMnet:11409876;iPTMnet:12091386;iPTMnet:14965474;iPTMnet:15116093',
None),
('CDH1',
'CTNNA1',
None,
'stimulation',
'HPRD:11226248;HPRD:7542250;InnateDB:11801604;InnateDB:16219695;InnateDB:9700170;IntAct:22750944;Lit-BM-17:10381631;Lit-BM-17:11960376;Lit-BM-17:16212417;Lit-BM-17:19016843;Lit-BM-17:25468996;Lit-BM-17:7542250;Lit-BM-17:8227214;Lit-BM-17:9233779;MPPI:9326449;SIGNOR:24336504;SPIKE:11226248;SPIKE:17145710;SPIKE_LC:11226248;SPIKE_LC:17145710',
None),
('PAK4',
'TP53',
None,
'stimulation',
'ProtMapper:27496712;iPTMnet:27496712',
None),
('CTNND1',
'CDH1',
None,
'stimulation',
'BioGRID:12427869;BioGRID:29207493;HPRD:10225956;HPRD:10409703;HPRD:10629228;HPRD:10931041;HPRD:11226248;HPRD:7542250;HPRD:7651399;InnateDB:17261850;InnateDB:8660921;Lit-BM-17:10409703;Lit-BM-17:12427869;Lit-BM-17:12640114;Lit-BM-17:12707304;Lit-BM-17:19711372;Lit-BM-17:20371349;Lit-BM-17:21670201;Lit-BM-17:22715382;Lit-BM-17:22752307;Lit-BM-17:22850631;Lit-BM-17:23180380;Lit-BM-17:24424122;Lit-BM-17:25468996;Lit-BM-17:7542250;Lit-BM-17:7651399;Lit-BM-17:7876318;Lit-BM-17:9535896;SIGNOR:14610055;SPIKE:20940130;SPIKE_LC:20940130',
None),
('WRN',
'TP53',
None,
'stimulation',
'BioGRID:11427532;HPRD:11399766;HPRD:11427532;HPRD:12080066;HPRD:15735006;IntAct:11427532;IntAct:15735006;Lit-BM-17:11427532;Lit-BM-17:12080066;Lit-BM-17:15735006;SPIKE:12080066;SPIKE:16713569;SPIKE_LC:12080066;SPIKE_LC:16713569',
None),
('SRC', 'MAPK11', None, 'stimulation', nan, None),
('SRC', 'PTP4A1', None, 'stimulation', nan, None),
('SRC',
'DAPK1',
None,
'inhibition',
'PhosphoSite:17803936;ProtMapper:21785723;ProtMapper:28976934;SPIKE:17803936;SPIKE_LC:17803936;iPTMnet:17803936',
None),
('TP53', 'SNAI2', None, 'stimulation', nan, None),
('SRC',
'PPP2CA',
None,
'inhibition',
'PhosphoSite:10978272;PhosphoSite:12921784;PhosphoSite:1325671;PhosphoSite:16286244;PhosphoSite:17303700;PhosphoSite:17394530;PhosphoSite:17635907;PhosphoSite:18208556;PhosphoSite:20558158;PhosphoSite:21292165;PhosphoSite:21554241;PhosphoSite:21791414;PhosphoSite:22299660;PhosphoSite:22771321;PhosphoSite:23222956;PhosphoSite:23251465;PhosphoSite:23436320;PhosphoSite:23926298;PhosphoSite:24395787;PhosphoSite:24676687;PhosphoSite:24997451;PhosphoSite:25003662;PhosphoSite:25726524;PhosphoSite:25931585;PhosphoSite:26378614;PhosphoSite:27013170;PhosphoSite:31992581;PhosphoSite:32130916;ProtMapper:23796501;SIGNOR:23796501;iPTMnet:23796501',
None),
('PRKCD',
'CDH1',
None,
'inhibition',
'ProtMapper:27203386;SIGNOR:27203386;iPTMnet:27203386',
None),
('HGF', 'SRC', None, 'stimulation', 'ProtMapper:23524339', None),
('SRC', 'GFRA1', None, 'stimulation', nan, None),
('GDNF', 'CDH1', None, 'stimulation', nan, None),
('S100A4',
'TP53',
None,
'stimulation',
'BioGRID:11527429;HPRD:11278647;HPRD:11527429;HPRD:12942774;HPRD:15116098;IntAct:19740107;IntAct:20591429;IntAct:23752197;IntAct:31837246;Lit-BM-17:11527429;Lit-BM-17:19740107;Lit-BM-17:20070253;Lit-BM-17:20591429;Lit-BM-17:23752197;SPIKE_LC:19740107',
None),
('NFKB1', 'TP53', None, 'stimulation', 'ACSN:8051093', None),
('PTP4A1', 'TP53', None, 'inhibition', nan, None),
('EZH2',
'CDH1',
None,
'inhibition',
'ACSN:11309385;ACSN:12508111;ACSN:14673164;ACSN:15169839;ACSN:17018611;ACSN:17615296;ACSN:19597490;ACSN:20519943;ACSN:20818389;ACSN:21685935;ACSN:22514743;ACSN:22796940;SPIKE:20574448;SPIKE_LC:20574448',
None),
('TP53',
'WRN',
None,
'inhibition',
'BioGRID:11427532;HPRD:11399766;HPRD:11427532;HPRD:12080066;HPRD:15735006;IntAct:11427532;IntAct:15735006;Lit-BM-17:11427532;Lit-BM-17:12080066;Lit-BM-17:15735006;SPIKE:12080066;SPIKE:16713569;SPIKE_LC:12080066;SPIKE_LC:16713569',
None),
('VAV1',
'SRC',
None,
'stimulation',
'Adhesome:1311423;Adhesome:1531699',
None),
('CDH1',
'SRC',
None,
'stimulation',
'ACSN:16039586;ACSN:16099633;ACSN:17143292;ACSN:17496910;ACSN:19029934;ACSN:19171760;ACSN:19619488;ACSN:19734908;ACSN:22007144;ACSN:22203675;ACSN:22370635;ACSN:23343194;BioGRID:10744074',
None),
('DAPK1',
'TP53',
None,
'stimulation',
'KEA:10801407;KEA:12111733;KEA:15254178;KEA:15489221;KEA:17339337;PhosphoSite:10606744;PhosphoSite:10673501;PhosphoSite:10733583;PhosphoSite:10734067;PhosphoSite:11244509;PhosphoSite:11258706;PhosphoSite:11707453;PhosphoSite:11883897;PhosphoSite:12091386;PhosphoSite:15355354;PhosphoSite:15542844;PhosphoSite:17339337;PhosphoSite:17977830;PhosphoSite:18246126;PhosphoSite:20851891;PhosphoSite:20959462;PhosphoSite:21386980;PhosphoSite:22112863;PhosphoSite:22815859;PhosphoSite:25584963;PhosphoSite:26742101;PhosphoSite:27753536;PhosphoSite:32266931;PhosphoSite:34168813;ProtMapper:17339337;ProtMapper:25229255;ProtMapper:26626260;ProtMapper:27681874;SIGNOR:17339337;iPTMnet:17297916;iPTMnet:17339337;phosphoELM:17339337',
None),
('EGF',
'SRC',
None,
'stimulation',
'ProtMapper:15845350;ProtMapper:19481075;ProtMapper:22927910;ProtMapper:23349873;ProtMapper:27462789',
None),
('SRC', 'ITGB4', None, 'stimulation', 'Adhesome:10592173', None),
('SRC', 'ITGB6', None, 'stimulation', 'Adhesome:10592173', None),
('GJA1', 'CDH1', None, 'stimulation', nan, None),
('TP53', 'AR', None, 'inhibition', 'SPIKE_LC:19481544', None),
('SRC',
'GRK2',
None,
'bimodal',
'CA1:11278940;HPRD:12624098;KEA:16725308;PhosphoSite:11566877;PhosphoSite:16725308;SIGNOR:16725308;SPIKE_LC:16189514;iPTMnet:16725308',
None),
('SRC', 'EPHB1', None, 'stimulation', nan, None),
('TP53',
'HSPA1A',
None,
'inhibition',
'HPRD:7811761;MPPI:8729618;SPIKE_LC:16713569',
None),
('SRC', 'NFKB1', None, 'stimulation', nan, None),
('SRC',
'PRKCD',
None,
'stimulation',
'HPRD:15337529;KEA:11927579;KEA:14715667;KEA:14970215;KEA:15541367;KEA:15961393;KEA:17570831;PhosphoSite:16982614;PhosphoSite:17658731;PhosphoSite:19366211;PhosphoSite:24211614;PhosphoSite:26876198;PhosphoSite:27203386;ProtMapper:10319993;ProtMapper:17658731;ProtMapper:18550549;ProtMapper:19138410;ProtMapper:19366211;ProtMapper:19632318;ProtMapper:22689788;ProtMapper:23329791;ProtMapper:23329794;ProtMapper:26876198;ProtMapper:27203386;ProtMapper:28637715;ProtMapper:29422059;ProtMapper:29452094;SPIKE_LC:15851033;iPTMnet:17569658',
None),
('ITGB8', 'SRC', None, 'stimulation', 'Adhesome:10592173', None),
('NUMB',
'TP53',
None,
'stimulation',
'BioGRID:23881403;DIP:18172499;IntAct:18172499;SIGNOR:18492217',
None),
('MAPK14',
'TP53',
None,
'stimulation',
'ACSN:11274345;ACSN:15140942;ACSN:15187187;ACSN:16393692;ACSN:19436832;ACSN:20506250;ACSN:21614932;BioGRID:21050851;HPRD-phos:10348343;HPRD-phos:10747897;HPRD-phos:10884347;HPRD-phos:19413330;InnateDB:10581258;KEA:10348343;KEA:10747897;KEA:1088347;KEA:10884347;KEA:16083285;KEA:16552184;KEA:9315650;Lit-BM-17:15642743;Lit-BM-17:17172861;Lit-BM-17:20213747;Lit-BM-17:21050851;Lit-BM-17:21675959;ProtMapper:10212189;ProtMapper:10581258;ProtMapper:10747897;ProtMapper:10781582;ProtMapper:11078726;ProtMapper:11258706;ProtMapper:11283254;ProtMapper:15642743;ProtMapper:15657900;ProtMapper:17535811;ProtMapper:17906639;ProtMapper:22975381;ProtMapper:24818748;ProtMapper:25789565;ProtMapper:26247731;SIGNOR:10581258;SIGNOR:10747897;SIGNOR:10781582;SIGNOR:11258706;SIGNOR:15642743;SIGNOR:17535811;SIGNOR:22975381;iPTMnet:10348343;iPTMnet:10581258;iPTMnet:10747897;iPTMnet:10781582;iPTMnet:10884347;iPTMnet:11258706;iPTMnet:15642743;iPTMnet:17535811;iPTMnet:19413330;iPTMnet:22975381',
None),
('SRC',
'CTNND1',
None,
'stimulation',
'HPRD-phos:11382764;HPRD-phos:14996911;HPRD-phos:17016520;HPRD-phos:17389395;HPRD-phos:18669648;HPRD-phos:18707149;HPRD-phos:20068231;HPRD:11382764;KEA:11382764;ProtMapper:11382764;ProtMapper:17194753;ProtMapper:19138410;ProtMapper:23457577;ProtMapper:26477567;SIGNOR:11382764;iPTMnet:11382764;iPTMnet:14996911;iPTMnet:17016520;iPTMnet:17194753;iPTMnet:17389395;iPTMnet:18669648;iPTMnet:18707149;iPTMnet:20068231',
None),
('PRKD1',
'CDH1',
None,
'stimulation',
'SIGNOR:15695390;SPIKE_LC:15695390',
None),
('CTNNA1', 'SRC', None, 'stimulation', nan, None),
('XIAP', 'TP53', None, 'stimulation', nan, None),
('RAP1A', 'CDH1', None, 'stimulation', nan, None),
('HMGB1',
'TP53',
None,
'stimulation',
'DIP:23063560;DIP:9472015;HPRD:11106654;HPRD:11748221;HPRD:9472015;IntAct:23063560;IntAct:9472015;Lit-BM-17:11106654;Lit-BM-17:11748221;Lit-BM-17:9472015;SPIKE_LC:16713569',
None),
('CDH1', 'RAP1A', None, 'stimulation', nan, None),
('SRC', 'HIPK2', None, 'stimulation', nan, None),
('SRC', 'TLN1', None, 'stimulation', nan, None),
('CDC42', 'CDH1', None, 'inhibition', nan, None),
('CDH1', 'ZYX', None, 'stimulation', nan, None),
('TP53', 'HSPA1B', None, 'inhibition', 'MPPI:8729618', None),
('SRC', 'PDGFD', None, 'stimulation', nan, None),
('GRK2',
'TP53',
None,
'stimulation',
'PhosphoSite:10933801;PhosphoSite:11409876;PhosphoSite:14729628;PhosphoSite:15053879;PhosphoSite:15116093;PhosphoSite:18952844;PhosphoSite:20124405;PhosphoSite:20473327;PhosphoSite:23723076;PhosphoSite:29988038;PhosphoSite:33256128;ProtMapper:20124405',
None),
('HSPA1B', 'TP53', None, 'inhibition', 'MPPI:8729618', None),
('SRC',
'FOS',
None,
'stimulation',
'PhosphoSite:17160021;PhosphoSite:22105363',
None),
('SRC',
'ITGB5',
None,
'stimulation',
'Adhesome:10592173;NetPath:19910644',
None),
('FGF2', 'TP53', None, 'inhibition', nan, None),
('SRC',
'AR',
None,
'stimulation',
'BioGRID:15027889;HPRD:15027889;HPRD:15062576;InnateDB:12933816;Lit-BM-17:15027889;Lit-BM-17:15062576;Lit-BM-17:15466214;Lit-BM-17:24728074;NetPath:11032808;NetPath:12933816;NetPath:15466214;ProtMapper:17525795;ProtMapper:19117998;ProtMapper:20383201;ProtMapper:20570899;ProtMapper:21318111;ProtMapper:21512132;ProtMapper:21886458;ProtMapper:21956655;ProtMapper:24859991;ProtMapper:24868554;ProtMapper:24948875;ProtMapper:25133482;ProtMapper:25547388;ProtMapper:25950519;ProtMapper:26829214;ProtMapper:28144231;SPIKE:17045208;SPIKE_LC:17045208',
None),
('PPP2CA',
'TP53',
None,
'bimodal',
'DEPOD:14712210;DEPOD:17245430;DEPOD:1848668;HPRD:12556559;ProtMapper:14712210;ProtMapper:17245430;SIGNOR:14712210;SIGNOR:17245430;SPIKE_LC:16713569',
None),
('TLN1', 'SRC', None, 'stimulation', nan, None),
('SRC', 'GDNF', None, 'stimulation', nan, None),
('SRC', 'MAPK3', None, 'stimulation', nan, None),
('PIK3R3',
'TP53',
None,
'stimulation',
'IntAct:32606738;SIGNOR:32606738',
None),
('TP53',
'S100A4',
None,
'stimulation',
'BioGRID:11527429;HPRD:11278647;HPRD:11527429;HPRD:12942774;HPRD:15116098;IntAct:19740107;IntAct:20591429;IntAct:23752197;IntAct:31837246;Lit-BM-17:11527429;Lit-BM-17:19740107;Lit-BM-17:20070253;Lit-BM-17:20591429;Lit-BM-17:23752197;SPIKE_LC:19740107',
None),
('SRC', 'MAPK14', None, 'stimulation', nan, None),
('NR3C1',
'TP53',
None,
'inhibition',
'BioGRID:11080152;HPRD:11080152;SPIKE_LC:16713569',
None),
('SRC', 'NUMB', None, 'stimulation', nan, None),
('ZYX', 'SRC', None, 'stimulation', nan, None),
('ITGB4', 'SRC', None, 'stimulation', 'Adhesome:10592173', None),
('TP53', 'GLI1', None, 'inhibition', nan, None),
('CDH1', 'EGF', None, 'inhibition', nan, None),
('SRC', 'FGF2', None, 'inhibition', nan, None),
('TP53',
'BCL2L1',
None,
'inhibition',
'BioGRID:24474649;DIP:24814347;HPRD:12667443;HPRD:16151013;IntAct:12667443;IntAct:14963330;IntAct:16151013;IntAct:24814347;Lit-BM-17:12667443;Lit-BM-17:14963330;Lit-BM-17:16151013;Lit-BM-17:20837658;Lit-BM-17:21900206;Lit-BM-17:24474649;Lit-BM-17:26556313;SPIKE_LC:16713569',
None),
('AR', 'CDH1', None, 'inhibition', nan, None),
('TP53',
'BCL6',
None,
'stimulation',
'SPIKE:16249378;SPIKE_LC:16249378',
None),
('HNRNPK',
'TP53',
None,
'stimulation',
'InnateDB:23092970;SPIKE:16360036;SPIKE:18472002;SPIKE_LC:16360036;SPIKE_LC:18472002',
None),
('ITGB5',
'SRC',
None,
'stimulation',
'Adhesome:10592173;NetPath:19910644',
None),
('SRC',
'PIK3R3',
None,
'stimulation',
'IntAct:25814554;Lit-BM-17:22402981;Lit-BM-17:25814554',
None),
('SRC',
'MET',
None,
'inhibition',
'BioGRID:9837958;HPRD:9837958;IntAct:24034250;IntAct:24728074;KEA:17570479;Lit-BM-17:24034250;Lit-BM-17:24728074;Lit-BM-17:9837958',
None),
('TP53', 'PDGFRB', None, 'inhibition', nan, None),
('SRC',
'PTK2B',
None,
'stimulation',
'Adhesome:10329689;Adhesome:10521452;Adhesome:10777553;Adhesome:11149930;Adhesome:11274221;Adhesome:12345678;Adhesome:14739300;Adhesome:14963038;Adhesome:19380485;Adhesome:8849729;Adhesome:9556630;Adhesome:9560226;CancerCellMap:14963038;HPRD:10777553;HPRD:8849729;InnateDB:14963038;IntAct:10521452;IntAct:11149930;IntAct:8849729;KEA:15070849;KEA:15585656;NetPath:14963038;PhosphoSite:12231407;PhosphoSite:12486027;PhosphoSite:12526812;PhosphoSite:15070849;PhosphoSite:15105428;PhosphoSite:15166227;PhosphoSite:15585656;PhosphoSite:15778498;PhosphoSite:19919693;PhosphoSite:22581436;PhosphoSite:25349423;PhosphoSite:31979355;ProtMapper:15695828;ProtMapper:18935208;ProtMapper:20001213;ProtMapper:20521079;ProtMapper:26866924;SIGNOR:15695828;SPIKE:14963038;SPIKE:16713569;SPIKE_LC:14963038;SPIKE_LC:16713569;SignaLink3:10593973;SignaLink3:12495636;SignaLink3:23109003;SignaLink3:7529876;dbPTM:12522270;dbPTM:17192257;dbPTM:17389395;dbPTM:18083107;dbPTM:19369195;dbPTM:19534553;dbPTM:20028775;dbPTM:20381867;dbPTM:20521079;iPTMnet:15695828;iPTMnet:20521079;iPTMnet:26866924',
None),
('SRC',
'PRKD1',
None,
'stimulation',
'HPRD:12637538;KEA:12637538;KEA:17804414;PhosphoSite:17804414;PhosphoSite:28842658;ProtMapper:12505989;ProtMapper:12637538;ProtMapper:17804414;ProtMapper:28174535;SIGNOR:12637538;SIGNOR:17804414;iPTMnet:12637538;iPTMnet:17804414;phosphoELM:17804414',
None),
('SRC', 'PAK4', None, 'stimulation', nan, None),
('FOS', 'TP53', None, 'inhibition', nan, None),
('TP53',
'HGF',
None,
'stimulation',
'SPIKE:18431400;SPIKE_LC:18431400',
None),
('EPHB1', 'SRC', None, 'stimulation', nan, None),
('GFRA1', 'CDH1', None, 'stimulation', nan, None),
('TP53', 'XIAP', None, 'stimulation', nan, None),
('MET',
'CDH1',
None,
'stimulation',
'ACSN:12040186;ACSN:14585353;ACSN:17496910;ACSN:19568798;ACSN:22558232;Cellinker:17336101;InnateDB:16909210',
None),
('SRC', 'ITGB8', None, 'stimulation', 'Adhesome:10592173', None),
('TP53',
'HMGB1',
None,
'stimulation',
'DIP:23063560;DIP:9472015;HPRD:11106654;HPRD:11748221;HPRD:9472015;IntAct:23063560;IntAct:9472015;Lit-BM-17:11106654;Lit-BM-17:11748221;Lit-BM-17:9472015;SPIKE_LC:16713569',
None),
('TP53',
'MET',
None,
'stimulation',
'SPIKE:18431400;SPIKE_LC:18431400',
None),
('HIPK2',
'TP53',
None,
'stimulation',
'BioGRID:11925430;BioGRID:22110707;HPRD-phos:11780126;HPRD-phos:11875057;HPRD-phos:16212962;HPRD:11780126;HPRD:11875057;HPRD:11925430;HPRD:15896780;IntAct:15896780;IntAct:16212962;KEA:11780126;KEA:11875057;KEA:16212962;KEA:16729035;Lit-BM-17:11740489;Lit-BM-17:11925430;Lit-BM-17:15896780;Lit-BM-17:16212962;Lit-BM-17:21057547;Lit-BM-17:25313037;ProtMapper:11740489;ProtMapper:11780126;ProtMapper:15865933;ProtMapper:16212962;ProtMapper:16601678;ProtMapper:17203463;ProtMapper:17210684;ProtMapper:17332358;ProtMapper:17349959;ProtMapper:17906639;ProtMapper:19128456;ProtMapper:19714248;ProtMapper:19731416;ProtMapper:19828042;ProtMapper:19946469;ProtMapper:20171273;ProtMapper:20418953;ProtMapper:20508833;ProtMapper:20849851;ProtMapper:21192925;ProtMapper:21258400;ProtMapper:21855806;ProtMapper:22110707;ProtMapper:22545114;ProtMapper:22889244;ProtMapper:22935610;ProtMapper:23091802;ProtMapper:23293771;ProtMapper:23316480;ProtMapper:23536002;ProtMapper:23700162;ProtMapper:23717325;ProtMapper:23814485;ProtMapper:23945296;ProtMapper:24101931;ProtMapper:24145406;ProtMapper:24211575;ProtMapper:24829283;ProtMapper:25210797;ProtMapper:25313037;ProtMapper:25364713;ProtMapper:26942128;ProtMapper:27019364;ProtMapper:27308326;ProtMapper:27308327;ProtMapper:27689990;ProtMapper:27787517;ProtMapper:27901482;ProtMapper:28107201;ProtMapper:28122345;ProtMapper:28893313;SIGNOR:17210684;SPIKE:17332358;SPIKE_LC:15896780;SPIKE_LC:16713569;SPIKE_LC:17332358;iPTMnet:11740489;iPTMnet:11780126;iPTMnet:11875057;iPTMnet:16212962;iPTMnet:16729035;iPTMnet:17203463;iPTMnet:17210684;iPTMnet:19828042;iPTMnet:22011578;phosphoELM:11780126;phosphoELM:16729035',
None),
('GLI1', 'TP53', None, 'inhibition', nan, None),
('SRC',
'CDC42',
None,
'stimulation',
'KEA:14506284;PhosphoSite:14506284;ProtMapper:14506284;ProtMapper:26816343;SIGNOR:14506284;SPIKE:9626657;SPIKE_LC:9626657;iPTMnet:14506284;phosphoELM:14506284',
None),
('HSPA1A',
'TP53',
None,
'inhibition',
'HPRD:7811761;MPPI:8729618;SPIKE_LC:16713569',
None),
('BCL2L1',
'TP53',
None,
'inhibition',
'BioGRID:24474649;DIP:24814347;HPRD:12667443;HPRD:16151013;IntAct:12667443;IntAct:14963330;IntAct:16151013;IntAct:24814347;Lit-BM-17:12667443;Lit-BM-17:14963330;Lit-BM-17:16151013;Lit-BM-17:20837658;Lit-BM-17:21900206;Lit-BM-17:24474649;Lit-BM-17:26556313;SPIKE_LC:16713569',
None),
('SRC',
'GJA1',
None,
'inhibition',
'ACSN:10679481;ACSN:10871288;ACSN:15534005;ACSN:15782139;ACSN:16492141;ACSN:9278444;ACSN:9592087;HPRD-phos:11514593;HPRD-phos:19901323;HPRD:11514593;HPRD:9278444;KEA:11514593;PhosphoSite:30448479;ProtMapper:11514593;ProtMapper:15350848;ProtMapper:16916748;ProtMapper:19284610;ProtMapper:21856279;ProtMapper:22342665;ProtMapper:23596415;ProtMapper:23718910;ProtMapper:24508467;ProtMapper:24670366;ProtMapper:26706150;ProtMapper:27280719;ProtMapper:29587860;ProtMapper:30095367;ProtMapper:30323740;SIGNOR:16916748;SPIKE_LC:16189514;iPTMnet:11514593;iPTMnet:16916748;iPTMnet:19901323',
None),
('SRC', 'MAPK1', None, 'stimulation', 'ProtMapper:17088251', None),
('BCL6',
'TP53',
None,
'inhibition',
'SPIKE:15577913;SPIKE_LC:15577913',
None),
('PDGFRB',
'SRC',
None,
'stimulation',
'BioGRID:18315570;HPRD:2173144;KEA:9010229;ProtMapper:15489898;SIGNOR:15489898;SPIKE_LC:16189514;iPTMnet:15489898;iPTMnet:9010229',
None),
('MAPK3',
'TP53',
None,
'stimulation',
'HPRD:10958792;InnateDB:10958792;PhosphoSite:10348343;PhosphoSite:10747897;PhosphoSite:11239457;PhosphoSite:12393879;PhosphoSite:17237827;PhosphoSite:18523266;PhosphoSite:24194938;PhosphoSite:25767119;PhosphoSite:28937686;PhosphoSite:9467949;PhosphoSite:9739174;ProtMapper:12955074;SIGNOR:12955074;SPIKE_LC:16713569;iPTMnet:10781582;iPTMnet:12955074',
None),
('SNAI2',
'CDH1',
None,
'inhibition',
'ACSN:11309385;ACSN:12508111;ACSN:14673164;ACSN:15169839;ACSN:17508028;ACSN:17615296;ACSN:19597490;ACSN:20519943;ACSN:20818389;ACSN:21685935;ACSN:22370643;ACSN:22796940',
None),
('SRC',
'VAV1',
None,
'stimulation',
'Adhesome:1311423;Adhesome:1531699',
None),
('PDGFD', 'SRC', None, 'stimulation', nan, None),
('PRKCD',
'TP53',
None,
'stimulation',
'IntAct:16377624;ProtMapper:16314418;ProtMapper:16377624;ProtMapper:17906639;SIGNOR:16377624;iPTMnet:16314418;iPTMnet:16377624',
None),
('SRC',
'HNRNPK',
None,
'bimodal',
'HPRD-phos:12052863;HPRD:12052863;HPRD:7516469;KEA:12052863;Lit-BM-17:16854432;Lit-BM-17:17178840;PhosphoSite:12052863;PhosphoSite:16854432;PhosphoSite:24642125;ProtMapper:12052863;ProtMapper:21184736;SIGNOR:12052863;SPIKE:12052863;SPIKE_LC:12052863;SPIKE_LC:16713569;SPIKE_LC:7592945;iPTMnet:12052863;phosphoELM:12052863',
None),
('SRC',
'RET',
None,
'stimulation',
'BioGRID:10070972;HPRD:10070972;KEA:11713247;KEA:17570479;SPIKE_LC:16189514',
None),
('DEK', 'TP53', None, 'stimulation', nan, None),
('TP53',
'NR3C1',
None,
'inhibition',
'BioGRID:11080152;HPRD:11080152;SPIKE_LC:16713569',
None),
('ITGB6', 'SRC', None, 'stimulation', 'Adhesome:10592173', None),
('EGF', 'CDH1', None, 'stimulation', nan, None),
('SRC', 'CTNNA1', None, 'stimulation', nan, None)],
'removed_edges': [('HGF',
'SRC',
None,
'stimulation',
'ProtMapper:23524339; ProtMapper:23524339',
None),
('PTK2B', 'RAC1', None, 'stimulation', 'Adhesome:10592173', None),
('EZH2',
'CDH1',
None,
'inhibition',
'ACSN:11309385;ACSN:12508111;ACSN:14673164;ACSN:15169839;ACSN:17018611;ACSN:17615296;ACSN:19597490;ACSN:20519943;ACSN:20818389;ACSN:21685935;ACSN:22514743;ACSN:22796940;SPIKE:20574448;SPIKE_LC:20574448; ACSN:11309385;ACSN:12508111;ACSN:14673164;ACSN:15169839;ACSN:17018611;ACSN:17615296;ACSN:19597490;ACSN:20519943;ACSN:20818389;ACSN:21685935;ACSN:22514743;ACSN:22796940;SPIKE:20574448;SPIKE_LC:20574448',
None),
('CDH1',
'SRC',
None,
'stimulation',
'ACSN:16039586;ACSN:16099633;ACSN:17143292;ACSN:17496910;ACSN:19029934;ACSN:19171760;ACSN:19619488;ACSN:19734908;ACSN:22007144;ACSN:22203675;ACSN:22370635;ACSN:23343194;BioGRID:10744074; ACSN:16039586;ACSN:16099633;ACSN:17143292;ACSN:17496910;ACSN:19029934;ACSN:19171760;ACSN:19619488;ACSN:19734908;ACSN:22007144;ACSN:22203675;ACSN:22370635;ACSN:23343194;BioGRID:10744074',
None),
('HGF', 'RAC1', None, 'stimulation', nan, None),
('TP53',
'HGF',
None,
'stimulation',
'SPIKE:18431400;SPIKE_LC:18431400; SPIKE:18431400;SPIKE_LC:18431400',
None),
('SRC',
'PTK2B',
None,
'stimulation',
'Adhesome:10329689;Adhesome:10521452;Adhesome:10777553;Adhesome:11149930;Adhesome:11274221;Adhesome:12345678;Adhesome:14739300;Adhesome:14963038;Adhesome:19380485;Adhesome:8849729;Adhesome:9556630;Adhesome:9560226;CancerCellMap:14963038;HPRD:10777553;HPRD:8849729;InnateDB:14963038;IntAct:10521452;IntAct:11149930;IntAct:8849729;KEA:15070849;KEA:15585656;NetPath:14963038;PhosphoSite:12231407;PhosphoSite:12486027;PhosphoSite:12526812;PhosphoSite:15070849;PhosphoSite:15105428;PhosphoSite:15166227;PhosphoSite:15585656;PhosphoSite:15778498;PhosphoSite:19919693;PhosphoSite:22581436;PhosphoSite:25349423;PhosphoSite:31979355;ProtMapper:15695828;ProtMapper:18935208;ProtMapper:20001213;ProtMapper:20521079;ProtMapper:26866924;SIGNOR:15695828;SPIKE:14963038;SPIKE:16713569;SPIKE_LC:14963038;SPIKE_LC:16713569;SignaLink3:10593973;SignaLink3:12495636;SignaLink3:23109003;SignaLink3:7529876;dbPTM:12522270;dbPTM:17192257;dbPTM:17389395;dbPTM:18083107;dbPTM:19369195;dbPTM:19534553;dbPTM:20028775;dbPTM:20381867;dbPTM:20521079;iPTMnet:15695828;iPTMnet:20521079;iPTMnet:26866924; Adhesome:10329689;Adhesome:10521452;Adhesome:10777553;Adhesome:11149930;Adhesome:11274221;Adhesome:12345678;Adhesome:14739300;Adhesome:14963038;Adhesome:19380485;Adhesome:8849729;Adhesome:9556630;Adhesome:9560226;CancerCellMap:14963038;HPRD:10777553;HPRD:8849729;InnateDB:14963038;IntAct:10521452;IntAct:11149930;IntAct:8849729;KEA:15070849;KEA:15585656;NetPath:14963038;PhosphoSite:12231407;PhosphoSite:12486027;PhosphoSite:12526812;PhosphoSite:15070849;PhosphoSite:15105428;PhosphoSite:15166227;PhosphoSite:15585656;PhosphoSite:15778498;PhosphoSite:19919693;PhosphoSite:22581436;PhosphoSite:25349423;PhosphoSite:31979355;ProtMapper:15695828;ProtMapper:18935208;ProtMapper:20001213;ProtMapper:20521079;ProtMapper:26866924;SIGNOR:15695828;SPIKE:14963038;SPIKE:16713569;SPIKE_LC:14963038;SPIKE_LC:16713569;SignaLink3:10593973;SignaLink3:12495636;SignaLink3:23109003;SignaLink3:7529876;dbPTM:12522270;dbPTM:17192257;dbPTM:17389395;dbPTM:18083107;dbPTM:19369195;dbPTM:19534553;dbPTM:20028775;dbPTM:20381867;dbPTM:20521079;iPTMnet:15695828;iPTMnet:20521079;iPTMnet:26866924',
None),
('SRC',
'RET',
None,
'stimulation',
'BioGRID:10070972;HPRD:10070972;KEA:11713247;KEA:17570479;SPIKE_LC:16189514; BioGRID:10070972;HPRD:10070972;KEA:11713247;KEA:17570479;SPIKE_LC:16189514',
None)],
'added_provenance': [],
'removed_provenance': []}
In [21]:
Copied!
net.checkout(1)
net.checkout(1)
In [27]:
Copied!
net.convert_edgelist_into_genesymbol()
net.convert_edgelist_into_genesymbol()
Out[27]:
| source | target | Type | Effect | References | Provenance | |
|---|---|---|---|---|---|---|
| 0 | CDH1 | SRC | None | stimulation | ACSN:16039586;ACSN:16099633;ACSN:17143292;ACSN... | None |
| 1 | SRC | RET | None | stimulation | BioGRID:10070972;HPRD:10070972;KEA:11713247;KE... | None |
| 2 | RET | CDH1 | None | stimulation | NaN | None |
| 3 | TP53 | HGF | None | stimulation | SPIKE:18431400;SPIKE_LC:18431400; SPIKE:184314... | None |
| 4 | HGF | SRC | None | stimulation | ProtMapper:23524339; ProtMapper:23524339 | None |
| 5 | SRC | PTK2B | None | stimulation | Adhesome:10329689;Adhesome:10521452;Adhesome:1... | None |
| 6 | PTK2B | TP53 | None | stimulation | NaN | None |
| 7 | TP53 | EZH2 | None | inhibition | NaN | None |
| 8 | EZH2 | CDH1 | None | inhibition | ACSN:11309385;ACSN:12508111;ACSN:14673164;ACSN... | None |
| 9 | CDH1 | RAC1 | None | stimulation | NaN | None |
| 10 | RAC1 | TP53 | None | stimulation | NaN | None |
| 11 | SRC | RAC1 | None | stimulation | ProtMapper:21798346;ProtMapper:22163037;ProtMa... | None |
| 12 | CDH1 | HGF | None | inhibition | NaN | None |
| 13 | RAC1 | CDH1 | None | inhibition | NaN | None |
| 14 | TP53 | RAC1 | None | inhibition | NaN | None |
| 15 | HGF | RAC1 | None | stimulation | NaN | None |
| 16 | PTK2B | RAC1 | None | stimulation | Adhesome:10592173 | None |
In [29]:
Copied!
net.add_node("MMP14")
net.add_node("CASP3")
net.add_node("MMP14")
net.add_node("CASP3")
Out[29]:
True
In [31]:
Copied!
net.connect_component(net.nodes["Genesymbol"].tolist(), ["MMP14", "CASP3"], maxlen=2, only_signed=True, consensus=True)
net.connect_component(net.nodes["Genesymbol"].tolist(), ["MMP14", "CASP3"], maxlen=2, only_signed=True, consensus=True)
In [ ]:
Copied!
HTML(net.history_html())
HTML(net.history_html())
In [ ]:
Copied!
HTML(net.history_html())
HTML(net.history_html())