Abstract
How the architecture of gene regulatory networks shapes gene expression patterns is an open question, which has been approached from a multitude of angles. The dominant strategy has been to identify nonrandom features in these networks and then argue for the function of these features using mechanistic modeling. Here we establish the foundation of an alternative approach by studying the correlation of network eigenvectors with synthetic gene expression data simulated with a basic and popular model of gene expression dynamics: Boolean threshold dynamics in signed directed graphs. We show that eigenvectors of the network adjacency matrix can predict collective states (attractors). However, the overall predictive power depends on details of the network architecture, namely the fraction of positive 3-cycles, in a predictable fashion. Our results are a set of statistical observations, providing a systematic step towards a further theoretical understanding of the role of network eigenvectors in dynamics on graphs.