Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Jul;35(Web Server issue):W613-8.
doi: 10.1093/nar/gkm287. Epub 2007 May 5.

MetaPath Online: a web server implementation of the network expansion algorithm

Thomas Handorf  1 , Oliver Ebenhöh
Affiliations

MetaPath Online: a web server implementation of the network expansion algorithm

Thomas Handorf et al. Nucleic Acids Res. 2007 Jul.

Abstract

We designed a web server for the analysis of biosynthetic capacities of metabolic networks. The implementation is based on the network expansion algorithm and the concept of scopes. For a given network and predefined external resources, called the seed metabolites, the scope is defined as the set of products which the network is in principle able to produce. Through the web interface the user can select a variety of metabolic networks or provide his or her own list of reactions. The information on the organism-specific networks has been extracted from the KEGG database. By choosing an arbitrary set of seed compounds, the user can obtain the corresponding scopes. With our web server application we provide an easy to use interface to perform a variety of structural and functional network analyses. Problems that can be addressed using the web server include the calculation of synthesizing capacities, the visualization of synthesis pathways, functional analysis of mutant networks or comparative analysis of related species. The web server is accessible through http://scopes.biologie.hu-berlin.de.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
The initial screen of MetaPath Online containing the input mask for the scope calculation.
Figure 2.
Figure 2.
Example expansion curve: shown is the expansion process on the reference network starting with ATP as seed.
Figure 3.
Figure 3.
Minimal synthesis path: the synthesis of citrate from pyruvate is shown. Irreversibility has been considered. The cofactors NAD+/NADH and CoA were available. The seed compounds (pyruvate, water and oxygen) are marked blue, the target metabolite (citrate) is marked red and the cofactors yellow.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006;34(Database issue):D354–D357. - PMC - PubMed
    1. Schomburg I, Chang A, Schomburg D. BRENDA, enzyme data and metabolic information. Nucleic Acids Res. 2002;30:47–49. - PMC - PubMed
    1. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, et al. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 2005;33:6083–6089. - PMC - PubMed
    1. Schuster S, Hilgetag C. On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 1994;2:165–182.
    1. Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 2000;18:326–332. - PubMed

Publication types

Substances