Related Experiment Video
Updated: Aug 23, 2025
05:01
A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
Published on: July 1, 2020
3.3K
KEGG for taxonomy-based analysis of pathways and genomes
Minoru Kanehisa1, Miho Furumichi1, Yoko Sato2
1Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
Nucleic Acids Research
|October 27, 2022
Summary
KEGG is a comprehensive biological database that integrates systems, genomic, chemical, and health information. Its updated features, including taxonomy mapping, enhance the analysis of gene conservation across diverse organisms.
Area of Science:
- Bioinformatics
- Systems Biology
- Genomics
Background:
- KEGG is a manually curated database integrating biological systems, genomic, chemical, and health information.
- Database entries are identified by KEGG identifiers (kid) and accessible via specific URL structures.
- KEGG provides viewers for pathways, Brite hierarchies, and genomes, facilitating data exploration.
Purpose of the Study:
- To describe the updated features of the KEGG database, focusing on improved genome representation and new analytical capabilities.
- To highlight the integration of an increasing number of eukaryotic genomes.
- To introduce the taxonomy mapping feature for comparative analysis across organism groups.
Main Methods:
- Manual curation of biological objects and integration into KEGG.
- Development of specific URL structures for accessing KEGG entries, pathways, hierarchies, and genomes.
- Implementation of an improved annotation procedure for KEGG Orthology (KO) assignment.
- Generation of multiple taxonomy files for organism and virus classification.
- Utilizing the Brite hierarchy viewer for taxonomy mapping within the KEGG Mapper suite.
Main Results:
- KEGG now includes a greater number of eukaryotic genomes, enhancing taxonomic representation.
- New KEGG Mapper suite features taxonomy mapping, a variant of Brite mapping.
- Taxonomy mapping allows for the analysis of conserved functional and physical gene links across organism groups.
- KEGG identifiers (kid) provide a standardized way to retrieve specific database entries.
Conclusions:
- The enhanced KEGG database, with its improved genome representation and taxonomy mapping, offers advanced tools for biological data analysis.
- KEGG facilitates the study of gene conservation and evolutionary relationships across a wide range of organisms.
- The database continues to be a vital resource for integrating and exploring diverse biological information.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
6.1K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.1K
01:29Modern Molecular Taxonomy
88
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
88
01:09Epistasis Analysis
5.1K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
5.1K
01:20Applications of Molecular Taxonomy
62
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
62
01:29Amino Acid Biosynthetic Pathways
85
Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
85