Impact of individual nodes in Boolean network dynamics Fakhteh - - PowerPoint PPT Presentation

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Impact of individual nodes in Boolean network dynamics Fakhteh Ghanbarnejad, Konstantin Klemm Bioinformatics group, Universitt Leipzig, Germany arXiv:1111.5334v1 Dresden, May 2012 Impact of individual nodes in Boolean network dynamics P.

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Impact of individual nodes in Boolean network dynamics

Fakhteh Ghanbarnejad, Konstantin Klemm

Bioinformatics group, Universität Leipzig, Germany

arXiv:1111.5334v1

Dresden, May 2012

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Impact of individual nodes in Boolean network dynamics

P. Oliveri, E. H. Davidson Current Opinion in Genetics & Development - 2004

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Regulatory Dynamics

M.H. Jensen, K. Sneppen, G. Tiana, FEBS Letters 541, 176 (2003)

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Regulatory Dynamics

parameters: production delay, production rates,

binding threshold, characteristic degradation times Hes1 & rna

six parameters for a single gene
larger systems?!!!

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Discrete Abstract Model

ON/Off States
Interactions Network
Dynamics (time evolution of states):

Logical Operators

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Attractors

A C B ABC 00 011 01 011 10 011 11 100 A C B A C B A C B A C B A C B A C B A C B A C B

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Activity & Sensitivity

F 00 0 F0 01 0 F1 10 1 F2 11 1 F3 F 10 F2 11 F3 00 F0 01 F1 F 00 1 F0 01 0 F1 10 1 F2 11 1 F3 F 10 F0 11 F3 00 F2 01 F1

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Impact of individual nodes in Boolean network dynamics

Short term Long term

Fakhteh Ghanbarnejad, Konstantin Klemm arXiv:1111.5334v1

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Computing the dynamical impact of nodes

1 1 1 1 1 1 1 1 1 1 1 1

Flip: 01 10

nand and and

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Variation of dynamical impact across nodes in random Boolean networks

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Predicting of dynamical impact

Why ?
S. Bornholdt. Science Vol. 310 no. 5747 pp. 449-451

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Predicting of dynamical impact

How ?

Fakhteh Ghanbarnejad, Konstantin Klemm arXiv:1111.5334v1

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Probabilistic description of damage spreading in a Boolean dynamics

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Impact of individual nodes in Boolean network dynamics

Centrality measures considered as predictors for the dynamical impact Range Adjacency matrix Activity matrix local

ut-degree

strength global eigenvector eigenvector

Fakhteh Ghanbarnejad, Konstantin Klemm arXiv:1111.5334v1

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Results for random Boolean networks

Range Adjacency matrix Activity matrix local

ut-degree

strength

global

eigenvector eigenvector

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Results for random Boolean networks

Range Adjacency matrix Activity matrix local

ut-degree

strength

global

eigenvector eigenvector

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Asynchronous updating
Attractor switching
With small perturbations

More cases

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Dynamical impact in a real network

fibroblast signal transduction

T. Helikaret al; PNAS 105, 1913 (2008)

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Impact of individual nodes in Boolean network dynamics

Range Adjacency matrix Activity matrix local

ut-degree

strength global eigenvector eigenvector

Fakhteh Ghanbarnejad, Konstantin Klemm arXiv:1111.5334v1

Linear algebra
Random Boolean networks
Empirical Boolean networks

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Thanks! To be continued …

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Fakhteh Ghanbarnejad Konstantin Klemm

Impact of individual nodes in Boolean network dynamics

arXiv:1111.5334v1

Stability of Boolean and continuous dynamics

Phys. Rev. Lett. 107.188701