Encyclopedic metabolic networks capture the sum of human knowledge of biochemical reactions and substrates as found across a multitude of organisms, and not one particular organism. A method for large-scale alignment of two such encyclopedic metabolic networks, KEGG and MetaCyc, has been designed to allow for a systematic comparison of their contents. A variety of methods for matching reactions...

Conservation of proximity of a pair of genes across multiple genomes generally indicates that their functions could be linked. Here, we present a systematic evaluation using 42 complete microbial genomes from 25 phylogenetic groups to test the reliability of this observation in predicting function for genes. We find a relationship between the number of phylogenetic groups in which a gene pair i...

New methodologies for performing pairwise tree-matching on carbohydrate sugar chain data were introduced in [3], in which well-known sequence alignment algorithms [12] were extended and an already known polynomial-time graph algorithm for finding the maximum common subtree (MCST) of two trees [7] was used to implement what is called the KEGG Carbohydrate Matcher, or KCaM. These new methodologie...

Objective(s): Schwann cells (SCs) have a wide range of applications as seed cells in the treatment of nerve injury during transplantation. However, there has been no report yet on kinds of proteomics changes that occur in Schwann cells before and after peripheral nerve injury.Materials and Methods: Activated Schwann cells (ASCs) and normal Schwann cells (NSCs) were obtained from adult Wistar ra...

Understanding cattle metabolism and its relationship with milk products is important in bovine breeding. A systemic view could lead to consequences that will result in a better understanding of existing concepts. Topological indices and quantitative characterizations mostly result from the application of graph theory on biological data. In the present work, the enzyme network involved in cattle...

One of the main challenges in systems biology is the establishment of the metabolome: a catalogue of the metabolites and biochemical reactions present in a specific organism. Current knowledge of biochemical pathways as stored in public databases such as KEGG, is based on carefully curated genomic evidence for the presence of specific metabolites and enzymes that activate particular biochemical...

One of the main challenges in systems biology is the establishment of the metabolome: a catalogue of the metabolites and biochemical reactions present in a specific organism. Current knowledge of biochemical pathways as stored in public databases such as KEGG, is based on carefully curated genomic evidence for the presence of specific metabolites and enzymes that activate particular biochemical...

R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the Reactome and KEGG databases. R spider implements a network-based statistical framework, which provides a global understanding of gene relations in the supplied gene list, and fully exploits the Reactome and KEGG knowledge bases. R spider ...

The emerging technology of DNA chips and microarrays makes it possible to simultaneously analyze the expression of many genes, such as the whole set of genes in the completely sequenced genome. We have been developing a system for network oriented analysis and visualization of such genome-scale gene expression data. It projects the time-series data of gene expression profiles on the functional ...