Subnetwork hierarchies of biochemical pathways

TL;DR

This paper introduces a method to decompose biochemical networks into hierarchical subnetworks, revealing core clusters and organizational patterns across multiple organisms, enhancing understanding of biochemical system architecture.

Contribution

The paper presents a novel geometric decomposition method for analyzing the hierarchical structure of biochemical networks across diverse organisms.

Findings

Metabolic networks form core clusters around highly connected substances.

Hierarchical organization includes well-defined subnetworks and outer shells.

Method applied successfully to 43 different organisms.

Abstract

We present a method to decompose biochemical networks into subnetworks based on the global geometry of the network. This method enables us to analyse the full hierarchical organisation of biochemical networks and is applied to 43 organisms from the WIT database. Two types of biochemical networks are considered: metabolic networks and whole-cellular networks (also including e.g. information processes). Conceptual and quantitative ways of describing the hierarchical ordering are discussed. The general picture of the metabolic networks arising from our study is that of a few core-clusters centred around the most highly connected substances enclosed by other substances in outer shells, and a few other well-defined subnetworks.