KEGG pathways

OGATA, H., GOTO, S., FUJIBUCHI, W., KANEHISA, M., Computation with the KEGG pathway database, BioSystems, 1998,47,119-128. 

II. KEGG Pathways and Ortholog Groups A. Gene Ontology... 

Fig. 3. Examples of the KEGG pathway diagrams a portion of the two-component signal transduction pathway and a portion of the metabolic pathway for nitrogen metabolism both in Escherichia coli.

The path computation has been most successful when applied to a specific class of binary relations, namely the substrate-product relations of enzymatic reactions. They constitute a well-characterized set of binary relations, and the amount of available data is relatively large. There are about 3,500 main reactions between the main compounds that are represented in the KEGG pathway diagrams. An enzymatic reaction generally involves multiple substrates and multiple products, so that it must first be decomposed into all possible substrate-product binary relations. However, because the relations involving ubiquitous compounds such as water and ATP will make many undesired connections, it is better to limit to main compounds for practical purposes. 

Assign KEGG pathway map names to the converted (Entrez-) genes. Obtain the four parameters for each pathway map in the same way as the GO terms. 

Fig. 3. Examples of input and output of SAMURAl-GUl system. An example of analysis with queries tnts (a) the CellMontage format as input and (b) graphical output of modules that share common biological function. Four example modules are searched by Benzbromarone, Fenbufen, Clofibrate, and Dichloroacetate. KEGG pathway functions for each module with the first and the second most significant p values are only shown.

Boehringer Mannheim EcoCyc KEGG, home KEGG Pathway site PathDB Soybase TRANSFAC American Type Culture Collection... 

Microarray DB Keio University Tool for mapping transcriptome data onto KEGG pathways and for creating a Web-based database with an overview of the entire pathway (http // www.g-language.org/data/marray/)... 

The analysis of network structure from the viewpoint of computer theory requires an introduction to some background information, which will be provided here. We will introduce the data involved for modeling metabolic pathways and the KEGG pathway database in particular. Furthermore, a basic introduction to graphs as used in computer science will be provided. 

KEGG http //www. genome. jp /kegg/pathway.html A pathway database... 

The last Web server, Paintomics, only allows joint visualization of preanalyzed and identified metabolites and genes, making it different from the two previous Web servers. Representations based on the KEGG pathways are completely rewritten with XML and SVG technology to allow a multiplexed data representation. This is the big advantage of Paintomics. 

H. Ogata, S. Goto, W. Eujibuchi, and M. Kanehisa, Computation with the KEGG pathway database. Biosystems 47(1-2) 119-128 (1998). 

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