Testing the results of Collombet et al.¶

Logical modeling of lymphoid and myeloid cellspecification and transdifferentiation¶

doi:https://www.pnas.org/content/114/23/5792

[1]:

import maboss
import maboss_test
from IPython.display import Image

[2]:

collombet_model = maboss.load("collombet.bnd", "collombet.cfg")

[3]:

test = maboss_test.MaBoSSTestCase(collombet_model)

Specification table¶

[4]:

Image(filename='table.png')

[4]:

_images/collombet_5_0.png

Stable states to observe¶

Here we define the states we want to observe:

[5]:

Mac = {'Mac1':1,'Flt3':0,'Cd19':0}

[6]:

Bcell = {'Mac1':0,'Flt3':0,'Cd19':1}

Test the possibility to be able to reach a state after a specific inhibition:¶

we will use the function “.assertStableStateProbability()” which will compare the probability that a set of nodes have a specific value, with a given probability (the default value for the comparison is 0)

‘Cebpa’:’ON’ ——>( Bcell -> Mac )¶

[7]:

test.assertStableStateProbability({'Cebpa':'ON'}, Mac, 'increase')

The reference probability is:  0
True!
The probability of reaching the state is: 0.32

[8]:

test.assertStableStateProbability({'Cebpa':'ON'}, Bcell, 'stable')

The reference probability is:  0
True!
The probability of reaching the state is: 0

‘Cebpa’:’ON’ and ‘Spi1’:’OFF’ ——>( Bcell -> all 0 )¶

[9]:

test.assertStableStateProbability({'Cebpa':'ON', 'Spi1_b1':'OFF'}, Mac,'stable')

The reference probability is:  0
True!
The probability of reaching the state is: 0

[10]:

test.assertStableStateProbability({'Cebpa':'ON', 'Spi1_b1':'OFF'}, Bcell, 'stable')

The reference probability is:  0
True!
The probability of reaching the state is: 0

‘Cebpa’:’ON’ and ‘Cebpa’:’OFF’——>( Bcell -> Mac )¶

[11]:

test.assertStableStateProbability({'Cebpa':'ON', 'Cebpb':'OFF'}, Mac,'increase')

The reference probability is:  0
True!
The probability of reaching the state is: 0.3206

[12]:

test.assertStableStateProbability({'Cebpa':'ON', 'Cebpb':'OFF'}, Bcell,'stable')

The reference probability is:  0
True!
The probability of reaching the state is: 0

‘Cebpa’:’ON’ and ‘Gfi1’:’ON’——>( Bcell -> Mac )¶

[13]:

test.assertStableStateProbability({'Cebpa':'ON', 'Gfi1':'ON'}, Mac,'increase')

The reference probability is:  0
True!
The probability of reaching the state is: 0.2031

[14]:

test.assertStableStateProbability({'Cebpa':'ON', 'Gfi1':'ON'}, Bcell,'stable')

The reference probability is:  0
True!
The probability of reaching the state is: 0

‘Cebpa’:’ON’ and ‘E2a’:’ON’——>( Bcell -> Mac )¶

[15]:

test.assertStableStateProbability({'Cebpa':'ON', 'E2a':'ON'}, Mac,'increase')

The reference probability is:  0
True!
The probability of reaching the state is: 0.3222

[16]:

test.assertStableStateProbability({'Cebpa':'ON', 'E2a':'ON'}, Bcell,'stable')

The reference probability is:  0
True!
The probability of reaching the state is: 0

‘Cebpa’:’ON’ and ‘Ebf1’:’ON’——>( Bcell -> Mac )¶

[17]:

test.assertStableStateProbability({'Cebpa':'ON', 'Ebf1':'ON'}, Mac,'increase')

The reference probability is:  0
True!
The probability of reaching the state is: 0.3538

[18]:

test.assertStableStateProbability({'Cebpa':'ON', 'Ebf1':'ON'}, Bcell,'stable')

The reference probability is:  0
True!
The probability of reaching the state is: 0

‘Cebpa’:’ON’ and ‘Foxo1’:’ON’——>( Bcell -> Mac )¶

[19]:

test.assertStableStateProbability({'Cebpa':'ON', 'Foxo1':'ON'}, Mac,'increase')

The reference probability is:  0
True!
The probability of reaching the state is: 0.2673

[20]:

test.assertStableStateProbability({'Cebpa':'ON', 'Foxo1':'ON'}, Bcell,'stable')

The reference probability is:  0
True!
The probability of reaching the state is: 0

‘Cebpa’:’ON’ and ‘Pax5’:’ON’——>( Bcell -> Mac )¶

[21]:

test.assertStableStateProbability({'Cebpa':'ON', 'Pax5':'ON'}, Mac,'increase')

The reference probability is:  0
True!
The probability of reaching the state is: 0.0756

[22]:

test.assertStableStateProbability({'Cebpa':'ON', 'Pax5':'ON'}, Bcell,'stable')

The reference probability is:  0
True!
The probability of reaching the state is: 0

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