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Open AccessJournal ArticleDOI

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 organization

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Journal ArticleDOI

Hypothesis-driven approach to predict transcriptional units from gene expression data

TL;DR: A co-clustering strategy of genome sequence information and gene expression data was applied to identify transcriptional units within diverse compendia of expression profiles and it is concluded that the suggested strategy will be amenable in general to the identification of transcriptionalunits beyond the chosen example of E.coli operons.
Journal ArticleDOI

Novel topological descriptors for analyzing biological networks

TL;DR: This study demonstrates that the application of entropic measures to molecules representing graphs is useful to characterize such structures meaningfully and finds that if one extends the measures for determining the structural information content of unlabeled graphs to labeled graphs, the uniqueness of the resulting indices is higher.
Book ChapterDOI

The cytomatrix as a cooperative system of macromolecular and water networks.

TL;DR: This chapter describes some prominent concepts of organized cell water, including vicinal water network theory, the association‐induction hypothesis, wave‐cluster theory, phase‐gel transition theories, and theories of low‐ and high‐density water polymorphs.
Journal ArticleDOI

Network Analysis-Based Approach for Exploring the Potential Diagnostic Biomarkers of Acute Myocardial Infarction.

TL;DR: A network analysis-based approach to analyze microarray expression profiling of peripheral blood in patients with AMI revealed and verified that NCF4, AQP9, NFIL3, DYSF, GZMA, TBX21, PRF1 and PTGDR genes by RT-qPCR may be potential candidates for diagnostic biomarker and possible regulatory targets in AMI.
Journal ArticleDOI

Incorporating gene co-expression network in identification of cancer prognosis markers

TL;DR: The weighted co-expression network is adopted to describe the interplay among genes and it is found that incorporating the network structure can improve cancer marker identification and have better prediction performance and reproducibility than genes identified using alternatives.
References
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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

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.
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