The achievements coming from genome analysis depend greatly on the quality of computational and processing methods. Tools for functional mRNA profiling and for gene information integration have become essential to this task. We have developed GeneBrowser as a novel approach that combines the advantages of mRNA profiling tools, at genome-scale experiments, with the features provided by data inte...

In this summary, I describe two topics on the subject of biochemical pathways. Recently, a Japanese research team devised a database for storing biological information at several different layers of abstraction. KEGG is one of the few databases storing current knowledge of biochemical pathways. In the first section, I give an overview of the KEGG database. The second item at study in this summa...

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 pro les on the functional r...

The definition of a phase shift of triplet periodicity (TP) is introduced. The mathematical algorithm for detection of TP phase shift of nucleotide sequences has been developed. Gene sequences from Kegg-46 data bank were analyzed with a purpose of searching genes with a phase shift of TP. The presence of a phase shift of triplet periodicity has been shown for 318329 genes (approximately 10% fro...

We have developed ClueGO, an easy to use Cytoscape plug-in that strongly improves biological interpretation of large lists of genes. ClueGO integrates Gene Ontology (GO) terms as well as KEGG/BioCarta pathways and creates a functionally organized GO/pathway term network. It can analyze one or compare two lists of genes and comprehensively visualizes functionally grouped terms. A one-click updat...

The comparison of metabolic pathway in different species is important in detecting a missing gene. There are many visualization tools for metabolic pathway. However, biologists need not only visualization of one pathway but also visualization for comparison among pathways. K-Viz is a tool for visualization of metabolic pathway based on KEGG. To compare among pathways in different species, K-Viz...

Motivation In many key applications in the field of metabolomics, such as toxicology or nutrigenomics, it is of interest to profile and detect physiological changes in metabolic pathways. For this purpose, it is useful to build a comprehensive graphical representation which shows metabolic processes occurring in an organism using networks. To model these systems it is possible to describe both ...

Pathway-level visualization of omics data provides an essential means for systems biology, to capture the systematic properties of the inner activities of cells. Here we describe a web-based resource consisting of a web-application for the visualization of complex omics data onto KEGG pathways to overview all entities in the context of cellular pathways, and databases created with the software ...