Pathway databases KEGG pathways

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

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... 

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

Modular analysis integrates the primary microarray analysis results and their functional annotations based on precompiled databases of pathways derived from large-scale literature analysis or computer-assisted annotation, such as Gene Ontology [39], KEGG [40], Biocarta (http //www.biocarta.com/), and GenMAPP [41]. 

Secondary metabolites are produced by plants in response to biotic or abiotic interactions with their environment and confer protection through a variety of antimicrobial, pesticidal, and pharmacological properties. Alkaloids are a class of plant secondary metabolites that traditionally have been classified as basic compounds derived firom amino acids that contain one or more heterocyclic nitrogen atom. About 20 % of plant species accumulate alkaloids, which are mostly derived from amino acids, e.g., phenylalanine, tyrosine, tryptophan, and lysine. The alkaloids are popular for their medicinal importance. The pharmaceutically important representatives of secondary metabolites are mostly alkaloids derived from tyrosine. In this chapter, we summarized the prior information, basic knowledge about the alkaloids, origin, physicochemical properties, uses, classification, biosynthetic reactions, and distribution of tyrosine-derived alkaloids especially opium alkaloids and their biosynthetic pathways in plants. We have also reviewed different web resources related to alkaloids and secondary metabolic pathway databases such as KEGG. 

Figure 1.3 Simplified pathways and network of the common sphingolipid classes and other related lipids. The network and the pathways are derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway databases. The pathways indicate the origins of sphingoid base core structures and their derivatives. Other sphingoid bases can be biosynthesized from other fatty acyl CoA by the replacement of palmitoyl CoA or some other amino acids replacing serine. The structures of individual lipid classes and their abbreviations used in the book are indicated in Figure 1.6.

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