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
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Integrated Systems Biology Approach Identifies Novel Maternal and Placental Pathways of Preeclampsia.
Nandor Gabor Than,Roberto Romero,Adi L. Tarca,Adi L. Tarca,Katalin A. Kékesi,Yi Xu,Zhonghui Xu,Zhonghui Xu,Kata Juhasz,Gaurav Bhatti,Ron Leavitt,Zsolt Gelencser,János Pálhalmi,Tzu Hung Chung,Balazs Gyorffy,László Orosz,Amanda Demeter,Anett Szecsi,Éva Hunyadi-Gulyás,Zsuzsanna Darula,Attila Simor,Katalin Éder,Szilvia Szabo,Szilvia Szabo,Vanessa Topping,Haidy El-Azzamy,Christopher LaJeunesse,Andrea Balogh,Andrea Balogh,Gabor Szalai,Gabor Szalai,Susan Land,Olga Török,Zhong Dong,Ilona Kovalszky,András Falus,Hamutal Meiri,Sorin Draghici,Sonia S. Hassan,Sonia S. Hassan,Tinnakorn Chaiworapongsa,Tinnakorn Chaiworapongsa,Manuel Krispin,Martin Knöfler,Offer Erez,Offer Erez,Offer Erez,Graham J. Burton,Chong Jai Kim,Chong Jai Kim,Chong Jai Kim,Gábor Juhász,Zoltán Papp +52 more
TL;DR: There are distinct maternal and placental disease pathways, and their interaction influences the clinical presentation of preeclampsia, and the description of these novel pathways in the “molecular phase” of preeClampsia and the identification of their hub molecules may enable timely molecular characterization of patients with distinct phenotypes.
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Back to the biology in systems biology: what can we learn from biomolecular networks?
TL;DR: To study the function of genes, it is necessary not only to see them in the context of gene networks, but also to reach beyond describing network topology and to embrace the global dynamics of networks that will reveal higher-order, collective behaviour of the interacting genes.
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Uncovering fuzzy community structure in complex networks.
TL;DR: A useful community detection method based on non-negative matrix factorization (NMF) technique is presented that can detect an appropriate number of fuzzy communities in which a node may belong to more than one community.
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Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes.
TL;DR: Genetic variation for phenotypic plasticity in the yeast transcriptome for the whole genome is investigated and significant genetic variation for transcriptional plasticity (GEI) among strains for approximately 5% of the genes in the genome is found.
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Biological impacts and context of network theory
TL;DR: It is expected that combining the currently separate layers of information from gene regulatory networks, signal transduction networks, protein interaction networks and metabolic networks will dramatically enhance the understanding of cellular function and dynamics.
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