One Hub-One Process: A Tool Based View on Regulatory Network Topology

TL;DR

This paper investigates the relationship between regulatory network topology and protein function in yeast, revealing that local network features reflect co-regulated proteins involved in similar tasks, shaped by biological processes.

Contribution

It provides a quantitative analysis linking network topology to protein function, highlighting how local features emerge from biological process requirements.

Findings

Weak remnants of network reorganization history.

Strong features of co-regulated proteins with similar functions.

Topology reflects biological process matching.

Abstract

The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for performance based localization on molecular networks. To quantify structure-function relationship we investigate similarities of proteins which are close in the regulatory network of the yeast Saccharomyces Cerevisiae. We find that the topology of the regulatory network show weak remnants of its history of network reorganizations, but strong features of co-regulated proteins associated to similar tasks. This suggests that local topological features of regulatory networks, including broad degree distributions, emerge as an implicit result of matching a number of needed processes to a finite toolbox of proteins.