Tikhonova Polina. Homework 2¶
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library(BoolNet)
my_network <- loadNetwork("boolnetwork.txt")
1 Bool network expressions¶
targets, factors
MBF, CLN3
SBF, (CLN3 | MBF) & ! (YOX1 & YHP1)
YOX1, MBF & SBF
HCM1, MBF & SBF
YHP1, MBF | SBF
SFF, SBF & HCM1
ACE2, SFF
SWI5, SFF
CLN3, (SWI5 & ACE2) & ! (YOX1 & YHP1)
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plotNetworkWiring(my_network)
2 Markov chains¶
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sim <- markovSimulation(my_network, numIterations=500)
sim # 6 states have a non-zero probability of being reached after 500 iterations
3 Attractors¶
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attr <- getAttractors(my_network)
print(attr, activeOnly=TRUE)
Baisins of attraction¶
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plotStateGraph(attr)
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par(mfrow=c(2, 1))
plotAttractors(attr)
All genes expressed initially¶
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attr_start_states <- getAttractors(my_network, startStates = list(rep(1,9)))
attr_start_states
plotAttractors(attr_start_states)
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path <- getPathToAttractor(my_network, rep(1,9))
plotSequence(sequence=path)
Asynchronous¶
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attr_asynchron <- getAttractors(my_network, type="asynchronous")
attr_asynchron
plotAttractors(attr_asynchron)
4 Other network¶
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my_new_network <- fixGenes(my_network, c("CLN3","MBF"), c(0,1))
other_attractors <- getAttractors(my_new_network)
plotAttractors(other_attractors)
