  To understand the system-wide organization of metabolism, different lines of
study have devised different categorizations of metabolites. The relationship
and difference between categories can provide new insights for a more detailed
description of the organization of metabolism. In this study, we investigate
the relative organization of three categorizations of metabolites -- pathways,
subcellular localizations and network clusters, by block-model techniques
borrowed from social-network studies and further characterize the categories
from topological point of view. The picture of the metabolism we obtain is that
of peripheral modules, characterized both by being dense network clusters and
localized to organelles, connected by a central, highly connected core.
Pathways typically run through several network clusters and localizations,
connecting them laterally. The strong overlap between organelles and network
clusters suggest that these are natural "modules" -- relatively independent
sub-systems. The different categorizations divide the core metabolism
differently suggesting that this, if possible, should be not be treated as a
module on par with the organelles. Although overlapping more than chance, none
of the pathways correspond very closely to a network cluster or localization.
This, we believe, highlights the benefits of different orthogonal
classifications and future experimental categorizations based on simple
principles.
