We consider a simplified model for gene regulation, where gene expression is regulated by transcription factors (TFs), which are single proteins or protein complexes. Proteins are in turn synthesised from expressed genes, creating a feedback loop of regulation. This leads to a directed bipartite network in which a link from a gene to a TF exists if the gene codes for a protein contributing to the TF, and a link from a TF to a gene exists if the TF regulates the expression of the gene. Both genes and TFs are modelled as binary variables, which indicate, respectively, whether a gene is expressed or not, and a TF is synthesised or not. We consider the scenario where for a TF to be synthesised, all of its contributing genes must be expressed. This results in an "AND" gate logic for the dynamics of TFs. By adapting percolation theory to directed bipartite graphs, evolving according to the AND logic dynamics, we are able to determine the region , in the network parameter space, where bipartite networks can support extensive gene expression , as required in stable cell types. In particular, the analysis reveals the possibility of a bi-stability region, where extensive gene expression can be either sustained or not sustained, depending on the initial network state, which is remarkably different from the transition observed in standard percolation theory. Finally, we investigate the resilience of global gene expression against node elimination protocols which mimic gene knockout experiments. Results reveal that gene regulatory networks inferred from gene knockout experiments may substantially differ from the network of effective gene-gene interactions extracted from the underlying bipartite graph .
We consider a simplified model for gene regulation, where gene expression is regulated by transcription factors (TFs), which are single proteins or protein complexes. Proteins are in turn synthesised from expressed genes, creating a feedback loop of regulation. This leads to a directed bipartite network in which a link from a gene to a TF exists if the gene codes for a protein contributing to the TF, and a link from a TF to a gene exists if the TF regulates the expression of the gene. Both genes and TFs are modelled as binary variables, which indicate, respectively, whether a gene is expressed or not, and a TF is synthesised or not. We consider the scenario where for a TF to be synthesised, all of its contributing genes must be expressed. This results in an ``AND'' gate logic for the dynamics of TFs. By adapting percolation theory to directed bipartite graphs, evolving according to the AND logic dynamics, we are able to determine the necessary conditions , in the network parameter space, under which bipartite networks can support a multiplicity of stable gene expression patterns, under noisy conditions, as required in stable cell types. In particular, the analysis reveals the possibility of a bi-stability region, where the extensive percolating cluster is or is not resilient to perturbations. This is remarkably different from the transition observed in standard percolation theory. Finally, we consider perturbations involving single node removal that mimic gene knockout experiments. Results reveal the strong dependence of the gene knockout cascade on the logic implemented in the underlying network dynamics, highlighting in particular that avalanche sizes cannot be easily related to gene-gene interaction networks .
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"AND"
``AND''
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region
necessary conditions
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where
under which
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extensive gene expression ,
a multiplicity of stable gene expression patterns, under noisy conditions,
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extensive gene expression can be either sustained or not sustained, depending on the initial network state, which
the extensive percolating cluster is or is not resilient to perturbations. This
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investigate the resilience of global gene expression against node elimination protocols which
consider perturbations involving single node removal that
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that gene regulatory networks inferred from gene knockout experiments may substantially differ from the network of effective
the strong dependence of the gene knockout cascade on the logic implemented in the underlying network dynamics, highlighting in particular that avalanche sizes cannot be easily related to
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interactions extracted from the underlying bipartite graph
interaction networks