Knockouts, Robustness and Cell Cycles

TL;DR

This paper investigates how Boolean threshold networks, including yeast cell cycle models, respond to node knockouts, revealing that the yeast network is not optimized for knockout resilience and that resilience weakly correlates with basin size.

Contribution

It introduces a framework for analyzing knockout resilience in Boolean networks and applies it to biological and synthetic sequences, including yeast cell cycle models.

Findings

Yeast cell cycle network is not optimized for knockout resilience.

Knockout resilience weakly correlates with basin of attraction size.

Analysis includes both random sequences and biological data.

Abstract

The response to a knockout of a node is a characteristic feature of a networked dynamical system. Knockout resilience in the dynamics of the remaining nodes is a sign of robustness. Here we study the effect of knockouts for binary state sequences and their implementations in terms of Boolean threshold networks. Beside random sequences with biologically plausible constraints, we analyze the cell cycle sequence of the species Saccharomyces cerevisiae and the Boolean networks implementing it. Comparing with an appropriate null model we do not find evidence that the yeast wildtype network is optimized for high knockout resilience. Our notion of knockout resilience weakly correlates with the size of the basin of attraction, which has also been considered a measure of robustness.