Having in mind the large-scale analysis of gene regulatory networks, we review a graph decimation algorithm, called “leaf-removal”, which can be used to evaluate the feedback in a random graph ensemble. In doing this, we consider the possibility of analyzing networks where the diagonal of the adjacency matrix is structured, that is, has a fixed number of nonzero entries. We test these ideas on a network model with fixed degree, using both numerical and analytical calculations. Our results are the following. First, the leaf-removal behavior for large system size enables to distinguish between different regimes of feedback. We show their relations and the connection with the onset of complexity in the graph. Second, the influence of the diagonal structure on this behavior can be relevant.

Randomization and feedback properties of directed graphs inspired to gene networks / M. Cosentino Lagomarsino, P. Jona, B. Bassetti (LECTURE NOTES IN COMPUTER SCIENCE). - In: Computational methods in systems biology / [a cura di] C. Priami. - [s.l] : Springer, 2006. - ISBN 978-3-540-46166-1. - pp. 227-241 [10.1007/11885191_16]

Randomization and feedback properties of directed graphs inspired to gene networks

M. Cosentino Lagomarsino
Primo
;
B. Bassetti
Ultimo
2006

Abstract

Having in mind the large-scale analysis of gene regulatory networks, we review a graph decimation algorithm, called “leaf-removal”, which can be used to evaluate the feedback in a random graph ensemble. In doing this, we consider the possibility of analyzing networks where the diagonal of the adjacency matrix is structured, that is, has a fixed number of nonzero entries. We test these ideas on a network model with fixed degree, using both numerical and analytical calculations. Our results are the following. First, the leaf-removal behavior for large system size enables to distinguish between different regimes of feedback. We show their relations and the connection with the onset of complexity in the graph. Second, the influence of the diagonal structure on this behavior can be relevant.
Settore FIS/02 - Fisica Teorica, Modelli e Metodi Matematici
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/31191
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