MetaCyc database http://metacyc.org/ MetaCyc is a database of metabolic pathways containing more than 1400 pathways from more than 1800 organisms. KEGG pathway database http://www.genome.jp/kegg/pathway.html The KEGG pathway database consists of a collection of manually-curated metabolic maps with connections to metabolite, enzyme and organismal data. KEGG also contains tools for reconstructing...

The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for linking genomes to biological systems,...

The number of complete and draft genomes has rapidly increased in recent years, and it has become increasingly important to identify the functional properties and biological roles of genes in these genomes. We have been developing KEGG Orthology (KO) to classify gene functions. In KO, we annotate genes in complete genomes based on best-hit information using Smith-Waterman scores, as well as by ...

BlastKOALA and GhostKOALA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct KEGG pathways, BRITE hierarchies and KEGG modules to infer high-level functions of the organism or the ecosystem. Both servers are made freely available at the KEGG Web site (http://www.kegg.jp/bla...

MOTIVATION KEGG PATHWAY is a service of Kyoto Encyclopedia of Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph models. While valuable graph tools have been implemented in R/Bioconductor, to our knowledge there is currently no software package to parse and analyze KEGG pathways with graph theory. RESULTS We in...

prostate cancer is the second most common cancer in men. in spite of on-going researches in this filed, the specific causes of prostate cancer are so far unknown. in this study, we used two methods of gene set analysis to improve the biological interpretation of the observed expression patterns in prostate cancer. the gene set analysis is a computational method to discover gene sets whose expre...