Talk:Metabolic network

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Untitled[edit]

Should not be redirected to Metabolism, a Metabolic network is a representation of the metabolism, and therefore a distinct entity. It is a tool used in Bioinformatics and Sytems biology.

Metabolic network = Pathway?[edit]

Is this the same thing as a metabolic pathway? There is no definition of what a metabilic network is. All the sentences are ambiguous and use complicated terms! -Pgan002 09:32, 4 October 2006 (UTC)[reply]

No, it is not the same, or to be more precise metabolic pathways are subsets of metabolic networks. Now I agree that the term metabolic network needs a clearer definition and maybe this article should be merged with Metabolic network modelling. Blastwizard 12:52, 4 October 2006 (UTC)[reply]

I would tend to agree with Blastwizard in theory. If we take a purist point of view, a pathway is directed while a network is not. And in biochemical pathway databases, there are often notions such as previous steps, next steps etc. THAT SAID, for the last three decades, the terms "metabolic network" and "metabolic pathway" have been consistently used interchangeably. There are no differences at all. A difference started to emerge more recently between metabolic networks and signaling pathways. Metabolic network is preferred by biochemists and modelers, because most metabolic reactions are fully reversible in physiological conditions. Therefore the "pathways" can proceed in both directions. The situation in Wikipedia is problematic at the moment. The main article is "metabolic pathway", but it describes "biochemical networks", neither solely metabolic, not strictly pathways. I believe the two articles should be worked upon together, and coordinated with "signal transduction" which is the redirection of "signaling pathway". Nicolas Le Novere (talk) 13:13, 16 November 2011 (UTC)[reply]

Merge[edit]

In papers such as this the term "metabolic network" is used as a synonym of "all the metabolic pathways in a cell". I think this page should therefore be merged with metabolism as a sub-section on "Prediction of metabolic networks". TimVickers 03:22, 5 March 2007 (UTC)[reply]

Disagree. I'm afraid, it is not because you have one reference (not publicly available) where the authors interchange the two terms that it should be merged, there is a subtle difference between a metabolic pathway and metabolic network, a pathway is a subset of a network in graph theory anyway. In addition, metabolic pathways are usually defined in a static manner, whereas metabolic networks can consider transient pathways via flux analysis. Blastwizard 09:48, 5 March 2007 (UTC)[reply]

My Oxford dictionary of Biochemistry and Mol Biology defines Metabolic pathway as "any series of connected (enzymatic or other) reactions occurring in a cell or organism." Is the difference between the complete set of metabolic pathways in a cell (its metabolism) and its metabolic network that the network contains protein interaction data, which are not chemical reactions? The definition here seems to imply this "An important asset to such analyses is the (partial) reconstruction of cellular networks, that is the collection and visualization of all potential physiologically relevant cellular processes. The reconstruction serves to sort the individual proteins, and thus the potential molecular functions, into a context (like pathways or protein complexes) and as such enables improved functional annotation."^[1] This also seems to be the sense the term is used here.^[2] I'll try a rewrite of this page to make it distinct from the metabolic pathways pages, otherwise this merge/delete discussion is going to come up again and again. TimVickers 17:28, 5 March 2007 (UTC)[reply]

Metabolic Network vs. Pathway[edit]

^ Francke C, Siezen R, Teusink B (2005). "Reconstructing the metabolic network of a bacterium from its genome". Trends Microbiol. 13 (11): 550–8. PMID 16169729.{{cite journal}}: CS1 maint: multiple names: authors list (link)
^ Eungdamrong N, Iyengar R (2004). "Computational approaches for modeling regulatory cellular networks". Trends Cell Biol. 14 (12): 661–9. PMID 15564042.

[1] Francke C, Siezen R, Teusink B (2005). "Reconstructing the metabolic network of a bacterium from its genome". Trends Microbiol. 13 (11): 550–8. PMID 16169729.{{cite journal}}: CS1 maint: multiple names: authors list (link)

[2] Eungdamrong N, Iyengar R (2004). "Computational approaches for modeling regulatory cellular networks". Trends Cell Biol. 14 (12): 661–9. PMID 15564042.

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