KEGG Bioinformatics Resource for Plant Genomics Research
Kyoto Encyclopedia of Genes and Genomes (KEGG) is a bioinformatics resource for understanding biological function from a genomic perspective. It is a multispecies, integrated resource consisting of genomic, chemical, and network information, with cross-references to numerous outside databases and containing a complete set of building blocks (genes and molecules) and wiring diagrams (biological pathways) to represent cellular functions. KEGG consists of a suite of databases: PATHWAY, GENES/Sequence Similarity Database (SSDB), Biomolecular Relations in Information Transmission and Expression (BRITE), and LIGAND, which is a composite database of COMPOUND, DRUG, GLYCAN, REACTION, REPAIR, and ENZYME. Two new databases have been recently added to KEGG: DGENES (for draft genomes) and EGENES (for expressed-sequence tag [EST] data). EGENES is a knowledge base system for efficient analysis of organism-specific ESTs, including publicly available plant ESTs. EGENES links the genomic information with higher order functional information in a single database. The genomic information stored in EGENES is a collection of EST contigs, produced by assembling the public ESTs. In this chapter, we will introduce KEGG and discuss its importance for the plant research community by focusing on EGENES. Because all the resources in KEGG follow the same architecture and design, an appraisal of EGENES should give readers an idea of the available information stored in KEGG and how to use them efficiently.
Key WordsPlant metabolic pathway EST assembly plant EST clustering functional annotation gene index transcriptome analysis EGENES
A JSPS Post Doctoral award from Laboratory of Plant Genetics and COE Post Doctoral award from Bioinformatics Center of Kyoto University to Ali Masoudi-Nejad are acknowledged. We also like to express our gratitude to Dr. Kiyoko F. Aoki-Kinoshita for critical reading of the manuscript.
- 7.Masoudi-Nejad, A., Jauregui, R., Kawashima, S., Goto, S., Kanehisa, M., and Endo, T.R. (2004) The kingdom of Plantae EST Indices: a resource for plant genomics community. Genome Informatics 2004. PP-102. The 15th International Conference on Genome Informatics December 16–18, 2004, Yokohama Pacifico, Japan.Google Scholar
- 8.Huang, X., and Madan, A. (1999) CAP3: a DNA sequence assembly program. Genome Res. 6, 829–845.Google Scholar