Coherent organization in gene regulation: a study on six networks

TL;DR

This study investigates the structural and dynamical features of gene regulatory networks, revealing a coherence principle where co-expressed genes with common targets tend to avoid conflicts, influenced by network parameters.

Contribution

It introduces the concept of coherence in gene regulation networks and analyzes its dependence on structural and dynamical parameters.

Findings

Genes with common targets are less conflicting at attractors.

Coherence depends on network parameters like input number and interaction ratio.

Dynamical measures such as basin size relate to coherence levels.

Abstract

Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation in three organisms or cell types each, and show that they obey a version of Hebb's rule which we term as coherence. More precisely, we find that simultaneously expressed genes with a common target are less likely to conflict at the attractors of the regulatory dynamics. We then investigate the dependence of coherence on structural parameters, such as the mean number of inputs per node and the activatory/repressory interaction ratio, as well as on dynamically determined quantities, such as the basin size and the number of expressed genes.