Usage¶

This notebook provides the steps to build a network starting from a list of genes, and using the default functionalities of NeKo.

In [1]:

%%time
from neko.core.network import Network
from neko._visual.visualize_network import NetworkVisualizer
import omnipath as op

%%time from neko.core.network import Network from neko._visual.visualize_network import NetworkVisualizer import omnipath as op

CPU times: user 3.58 s, sys: 898 ms, total: 4.48 s
Wall time: 4.48 s

1. Define the list of genes of interest¶

In [2]:

genes = ["SRC", "NOTCH1", "FAK", "CDH1", "CDH2", "VIM", "MAP4K4", "LATS1", "LATS2", "PTK2B"]

genes = ["SRC", "NOTCH1", "FAK", "CDH1", "CDH2", "VIM", "MAP4K4", "LATS1", "LATS2", "PTK2B"]

2. Create a network using as input the gene set.¶

Note

NB! If no resource is specified, the default used resource by the package is omnipath.interactions.Omnipath(). To add new resources, please see the Add resources tutorial.

2A. Import genes as network nodes¶

In [12]:

new_net1 = Network(genes, resources = 'omnipath')

new_net1 = Network(genes, resources = 'omnipath')

In [13]:

#Print node dataframe
new_net1.nodes

#Print node dataframe new_net1.nodes

Out[13]:

	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

2B. Explore if the nodes are connected without introducing new intermidiate nodes¶

In [14]:

%%time
new_net1.connect_nodes(only_signed=True, consensus_only=True)

%%time new_net1.connect_nodes(only_signed=True, consensus_only=True)

CPU times: user 189 ms, sys: 6 μs, total: 189 ms
Wall time: 188 ms

2C. Visualize the network with the following command.¶

The network picture is also exported in the working repository, in pdf format.

In [15]:

visualizer = NetworkVisualizer(new_net1, color_by='effect', noi=True)
visualizer.render()

visualizer = NetworkVisualizer(new_net1, color_by='effect', noi=True) visualizer.render()

2D. Connect disconnected nodes by importing intermediate nodes.¶

maxlen is the mandatory maximum path length in edges.

path_policy controls which resource paths are selected when a connection is missing: one_shortest selects one stable shortest path, all_shortest selects the edge union of every shortest alternative, and all_bounded selects every simple path through maxlen.

reuse_policy controls which topology can prevent later searches: none keeps pair searches independent, discovered_paths reuses explicitly selected paths, and induced_subgraph also exposes direct resource interactions among all selected nodes.

only_signed restricts the search to signed interactions. consensus requires sign consensus between references when the resource provides it. Stable unweighted ordering improves reproducibility but is not a biological ranking.

In [ ]:

%%time
new_net1.complete_connection(maxlen=3, path_policy="one_shortest", reuse_policy="discovered_paths", only_signed=True, consensus=True)

%%time new_net1.complete_connection(maxlen=3, path_policy="one_shortest", reuse_policy="discovered_paths", only_signed=True, consensus=True)

3. Visualize final network¶

In [18]:

#Visualize a specific nodes and 
visualizer1 = NetworkVisualizer(new_net1,color_by='effect', noi=True)
visualizer1.render()

#Visualize a specific nodes and visualizer1 = NetworkVisualizer(new_net1,color_by='effect', noi=True) visualizer1.render()

In [9]:

#Visualize a specific nodes and 
visualizer1 = NetworkVisualizer(new_net1, predefined_node = "SRC",color_by='effect')
visualizer1.render()

#Visualize a specific nodes and visualizer1 = NetworkVisualizer(new_net1, predefined_node = "SRC",color_by='effect') visualizer1.render()

In [17]:

#We can access to the edges of the network
new_net1.edges

#We can access to the edges of the network new_net1.edges

Out[17]:

	source	target	Type	Effect	References	Provenance
0	P12931	Q05397	None	stimulation	Adhesome:10085298;Adhesome:10592173;Adhesome:1...	None
1	P12830	P12931	None	stimulation	ACSN:16039586;ACSN:16099633;ACSN:17143292;ACSN...	None
2	P12931	P19022	None	inhibition	ACSN:15782139;ACSN:16371504;ACSN:16492141;ACSN...	None
3	P12931	Q14289	None	stimulation	Adhesome:10329689;Adhesome:10521452;Adhesome:1...	None
4	Q14289	Q05397	None	stimulation	Adhesome:16760434;HPRD:16760434;KEA:12960434;K...	None
...	...	...	...	...	...	...
221	P01106	O95863	None	stimulation	NaN	None
222	P61586	P42336	None	stimulation	NaN	None
223	P42336	P61586	None	stimulation	NaN	None
224	P05305	P61586	None	stimulation	NaN	None
225	Q13043	O15151	None	stimulation	NaN	None

226 rows × 6 columns

In [ ]: