Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms

Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A (2008)
NUCLEIC ACIDS RESEARCH 36(Web Server): W433-W437.

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Journal Article | Published | English
Abstract
In order to understand the phenotype of any living system, it is essential to not only investigate its genes, but also the specific metabolic pathway variant of the organism of interest, ideally in comparison with other organisms. The Comparative Pathway Analyzer, CPA, calculates and displays the differences in metabolic reaction content between two sets of organisms. Because results are highly dependent on the distribution of organisms into these two sets and the appropriate definition of these sets often is not easy, we provide hierarchical clustering methods for the identification of significant groupings. CPA also visualizes the reaction content of several organisms simultaneously allowing easy comparison. Reaction annotation data and maps for visualizing the results are taken from the KEGG database. Additionally, users can upload their own annotation data. This website is free and open to all users and there is no login requirement. It is available at https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html.
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Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A. Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. NUCLEIC ACIDS RESEARCH. 2008;36(Web Server):W433-W437.
Oehm, S., Gilbert, D., Tauch, A., Stoye, J., & Goesmann, A. (2008). Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. NUCLEIC ACIDS RESEARCH, 36(Web Server), W433-W437.
Oehm, S., Gilbert, D., Tauch, A., Stoye, J., and Goesmann, A. (2008). Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. NUCLEIC ACIDS RESEARCH 36, W433-W437.
Oehm, S., et al., 2008. Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. NUCLEIC ACIDS RESEARCH, 36(Web Server), p W433-W437.
S. Oehm, et al., “Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms”, NUCLEIC ACIDS RESEARCH, vol. 36, 2008, pp. W433-W437.
Oehm, S., Gilbert, D., Tauch, A., Stoye, J., Goesmann, A.: Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. NUCLEIC ACIDS RESEARCH. 36, W433-W437 (2008).
Oehm, Sebastian, Gilbert, David, Tauch, Andreas, Stoye, Jens, and Goesmann, Alexander. “Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms”. NUCLEIC ACIDS RESEARCH 36.Web Server (2008): W433-W437.
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PMID: 25887214
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PMID: 25202338
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12 References

Data provided by Europe PubMed Central.

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation
Forst CV, Flamm C, Hofacker I, Stadler P., 2006
Conserved pathways within bacteria and yeast as revealed by global protein network alignment.
Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker T., Proc. Natl. Acad. Sci. U.S.A. 100(20), 2003
PMID: 14504397
PathBLAST: a tool for alignment of protein interaction networks.
Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215356
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD., Nucleic Acids Res. 36(Database issue), 2008
PMID: 17965431
KEGG for linking genomes to life and the environment.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y., Nucleic Acids Res. 36(Database issue), 2008
PMID: 18077471
EMBL Nucleotide Sequence Database in 2006.
Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G, Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler R., Nucleic Acids Res. 35(Database issue), 2007
PMID: 17148479

Everitt BS, Landau S, Leese M., 2001
Hierarchical grouping to optimize an objective function.
Ward JH., 1963
The comparison of dendrograms by objective methods
Sokal RR, Rohlf FJ., 1962
Differential genome analyses of metabolic enzymes in Pseudomonas aeruginosa for drug target identification.
Perumal D, Lim CS, Sakharkar KR, Sakharkar MK., In Silico Biol. (Gedrukt) 7(4-5), 2007
PMID: 18391237
Characterization of the alanine racemases from Pseudomonas aeruginosa PAO1.
Strych U, Huang HC, Krause KL, Benedik MJ., Curr. Microbiol. 41(4), 2000
PMID: 10977898

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