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

被引：20

作者：

Handorf, Thomas ^{[2
]}

Ebenhoeh, Oliver ^{[1
]}

机构：

[1] Univ Hosp Charite Berlin, Inst Biochem, D-10117 Berlin, Germany

[2] Humboldt Univ, Dept Theoret Biophys, Inst Biol, D-10115 Berlin, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

关键词：

D O I：

10.1093/nar/gkm287

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：W613 / W618

页数：6

共 15 条

[1] Evolutionary changes of metabolic networks and their biosynthetic capacities [J].

Ebenhoeh, O. ;

Handorf, T. ;

Kahn, D. .

IEE PROCEEDINGS SYSTEMS BIOLOGY, 2006, 153 (05) :354-358

[2]

Ebenhoh Oliver, 2006, Genome Inform, V17, P163

[3]

Ebenhoh Oliver, 2005, Genome Inform, V16, P203

[4] A TECHNIQUE FOR DRAWING DIRECTED-GRAPHS [J].

GANSNER, ER ;

KOUTSOFIOS, E ;

NORTH, SC ;

VO, KP .

IEEE TRANSACTIONS ON SOFTWARE ENGINEERING, 1993, 19 (03) :214-230

[5] Hierarchy of metabolic compounds based on their synthesising capacity [J].

Handorf, T. ;

Ebenhoeh, O. ;

Kahn, D. ;

Heinrich, R. .

IEE PROCEEDINGS SYSTEMS BIOLOGY, 2006, 153 (05) :359-363

[6] Expanding metabolic networks:: Scopes of compounds, robustness, and evolution [J].

Handorf, T ;

Ebenhöh, O ;

Heinrich, R .

JOURNAL OF MOLECULAR EVOLUTION, 2005, 61 (04) :498-512

[7] The large-scale organization of metabolic networks [J].

Jeong, H ;

Tombor, B ;

Albert, R ;

Oltvai, ZN ;

Barabási, AL .

NATURE, 2000, 407 (6804) :651-654

[8] From genomics to chemical genomics: new developments in KEGG [J].

Kanehisa, Minoru ;

Goto, Susumu ;

Hattori, Masahiro ;

Aoki-Kinoshita, Kiyoko F. ;

Itoh, Masumi ;

Kawashima, Shuichi ;

Katayama, Toshiaki ;

Araki, Michihiro ;

Hirakawa, Mika .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D354-D357

[9] Expansion of the BioCyc collection of pathway/genome databases to 160 genomes [J].

Karp, PD ;

Ouzounis, CA ;

Moore-Kochlacs, C ;

Goldovsky, L ;

Kaipa, P ;

Ahrén, D ;

Tsoka, S ;

Darzentas, N ;

Kunin, V ;

López-Bigas, N .

NUCLEIC ACIDS RESEARCH, 2005, 33 (19) :6083-6089

[10] Advances in flux balance analysis [J].

Kauffman, KJ ;

Prakash, P ;

Edwards, JS .

CURRENT OPINION IN BIOTECHNOLOGY, 2003, 14 (05) :491-496

← 1 2 →