Hierarchical Organization of Modularity in Metabolic Networks
TLDR
It is shown that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law.Abstract:
Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated biochemical networks lacks quantitative support Here, we show that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law Within Escherichia coli, the uncovered hierarchical modularity closely overlaps with known metabolic functions The identified network architecture may be generic to system-level cellular organizationread more
Citations
More filters
Journal ArticleDOI
Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks
Mikael Huss,Petter Holme +1 more
TL;DR: It is argued that cross-modular edges are the key for the robustness of metabolism, found to be more modular than random networks but far from perfectly divisible into modules.
Journal ArticleDOI
Polyanions and the Proteome
TL;DR: It is argued that future understanding of the proteome will require that the “polyanion world” be taken into account and that many hundreds to thousands of such interactions are present in cells.
Journal ArticleDOI
HIF-1α is required for disturbed flow-induced metabolic reprogramming in human and porcine vascular endothelium
David Wu,Ru-Ting Huang,Robert B. Hamanaka,Matthew Krause,Myung-Jin Oh,Cheng Hsiang Kuo,Recep Nigdelioglu,Angelo Y. Meliton,Leah J. Witt,Guohao Dai,Mete Civelek,Nanduri R. Prabhakar,Yun Fang,Gökhan M. Mutlu +13 more
TL;DR: Using transcriptomics and bioenergetic analysis, it is discovered that DF induces glycolysis and reduces mitochondrial respiratory capacity in human aortic ECs, highlighting a previously uncharacterized role for flow-induced metabolic reprogramming and inflammation in ECs.
Journal ArticleDOI
A systematic approach to the one-mode projection of bipartite graphs
TL;DR: A systematic approach is presented that evaluates the significance of the co-occurrence for each pair of nodes v, w, i.e., the number of common neighbors of v and w and shows stable and significant results that result in attractive one-mode projections of bipartite graphs.
Journal ArticleDOI
Hospital Networks and the Dispersal of Hospital-Acquired Pathogens by Patient Transfer
TL;DR: The results indicate that hospitals cannot be viewed as individual units but rather should be views as connected elements of larger modular networks and the importance of cooperative effects that will have a bearing on the planning of health care systems, patient management and hospital infection control.
References
More filters
Journal ArticleDOI
Collective dynamics of small-world networks
TL;DR: Simple models of networks that can be tuned through this middle ground: regular networks ‘rewired’ to introduce increasing amounts of disorder are explored, finding that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.
Journal ArticleDOI
Emergence of Scaling in Random Networks
TL;DR: A model based on these two ingredients reproduces the observed stationary scale-free distributions, which indicates that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.
Journal ArticleDOI
Statistical mechanics of complex networks
TL;DR: In this paper, a simple model based on the power-law degree distribution of real networks was proposed, which was able to reproduce the power law degree distribution in real networks and to capture the evolution of networks, not just their static topology.
Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Journal ArticleDOI
Community structure in social and biological networks
Michelle Girvan,Mark Newman +1 more
TL;DR: This article proposes a method for detecting communities, built around the idea of using centrality indices to find community boundaries, and tests it on computer-generated and real-world graphs whose community structure is already known and finds that the method detects this known structure with high sensitivity and reliability.