Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks
In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work, we investigate to what extent these findings apply to metabolic networks. To this end, we...
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| Veröffentlicht in: | EURASIP journal on bioinformatics & systems biology 2009, Vol.2009 (1), p.630695-15 |
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| creator | van Nes, P. Bellomo, D. Reinders, M.J.T. de Ridder, D. |
| description | In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work, we investigate to what extent these findings apply to metabolic networks. To this end, we extend a previously proposed method by changing the null model for determining motif enrichment, by using interaction types directly obtained from structural interaction matrices, by generating a distribution of partial derivatives of reaction rates and by simulating enzymatic regulation on metabolic networks. Our findings suggest that the conclusions drawn in previous work cannot be extended to metabolic networks, that is, structurally stable network motifs are not enriched in metabolic networks. |
| doi_str_mv | 10.1155/2009/630695 |
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It was shown that structurally stable network motifs are enriched in such networks. In this work, we investigate to what extent these findings apply to metabolic networks. To this end, we extend a previously proposed method by changing the null model for determining motif enrichment, by using interaction types directly obtained from structural interaction matrices, by generating a distribution of partial derivatives of reaction rates and by simulating enzymatic regulation on metabolic networks. Our findings suggest that the conclusions drawn in previous work cannot be extended to metabolic networks, that is, structurally stable network motifs are not enriched in metabolic networks.</description><identifier>ISSN: 1687-4145</identifier><identifier>EISSN: 1687-4153</identifier><identifier>DOI: 10.1155/2009/630695</identifier><identifier>PMID: 19197379</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Biomedical Engineering and Bioengineering ; Computational Biology/Bioinformatics ; E coli ; Engineering ; Genetics ; Metabolism ; Metabolites ; Modelling ; Network Structure and Biological Function: Reconstruction ; Research Article ; Signal,Image and Speech Processing ; Statistical Approaches ; Systems Biology</subject><ispartof>EURASIP journal on bioinformatics & systems biology, 2009, Vol.2009 (1), p.630695-15</ispartof><rights>P. van Nes et al. 2009. This article is published under license to BioMed Central Ltd. 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This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</rights><rights>Copyright © 2009 P. van Nes et al. 2009 P. van Nes et al.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3905-bebd2ab7bafefc80c22939b6adf71fd2b1e8c7ebbaf5c14bbb78db861ece36f03</citedby><cites>FETCH-LOGICAL-c3905-bebd2ab7bafefc80c22939b6adf71fd2b1e8c7ebbaf5c14bbb78db861ece36f03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171437/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171437/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,4024,27923,27924,27925,41120,42189,51576,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19197379$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>van Nes, P.</creatorcontrib><creatorcontrib>Bellomo, D.</creatorcontrib><creatorcontrib>Reinders, M.J.T.</creatorcontrib><creatorcontrib>de Ridder, D.</creatorcontrib><title>Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks</title><title>EURASIP journal on bioinformatics & systems biology</title><addtitle>J Bioinform Sys Biology</addtitle><addtitle>EURASIP J Bioinform Syst Biol</addtitle><description>In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work, we investigate to what extent these findings apply to metabolic networks. To this end, we extend a previously proposed method by changing the null model for determining motif enrichment, by using interaction types directly obtained from structural interaction matrices, by generating a distribution of partial derivatives of reaction rates and by simulating enzymatic regulation on metabolic networks. Our findings suggest that the conclusions drawn in previous work cannot be extended to metabolic networks, that is, structurally stable network motifs are not enriched in metabolic networks.</description><subject>Biomedical Engineering and Bioengineering</subject><subject>Computational Biology/Bioinformatics</subject><subject>E coli</subject><subject>Engineering</subject><subject>Genetics</subject><subject>Metabolism</subject><subject>Metabolites</subject><subject>Modelling</subject><subject>Network Structure and Biological Function: Reconstruction</subject><subject>Research Article</subject><subject>Signal,Image and Speech Processing</subject><subject>Statistical Approaches</subject><subject>Systems 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| subjects | Biomedical Engineering and Bioengineering Computational Biology/Bioinformatics E coli Engineering Genetics Metabolism Metabolites Modelling Network Structure and Biological Function: Reconstruction Research Article Signal,Image and Speech Processing Statistical Approaches Systems Biology |
| title | Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks |
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