Long loops of information flow in genetic networks highlight an inherent directionality

Abstract

Genetic networks integrate the reported interactions between genes into a global view of the transcription regulation. These networks contain, beyond each specific interaction, the information flow between genes and groups of genes that determine the cellular response to different stimuli. The flow of information in such networks is based on the structure of the directed interactions paths, and is not obviously decipherable from the number of paths between genes in the network, which grows exponentially with the number of nodes. We show here that the directional large scale information flow in genetic networks can be understood by combining the cycle (closed walk in graph theory terms) length and distance distributions. These properties are highly sensitive to the effect of flipping the direction of a small number of random edges. Here we focus on cycles composed of back and forth minimal paths between a pair of nodes that we further denote as loops. Intra-cellular networks contain a surprisingly large nu...