What is the difference between gene Ontology and KEGG?
What is the difference between gene Ontology and KEGG?
KEGG, Panther and other “pathway” databases group genes into “pathways” which are basically lists of genes participating in the same biological process. Ontology annotations give more flexibility and capture better (in my view) the complexity of gene functional relationships.
What is a KEGG pathway analysis?
KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge of the molecular interaction, reaction and relation networks for: 1. Metabolism. Global/overview Carbohydrate Energy Lipid Nucleotide Amino acid Other amino Glycan.
What is KEGG bioinformatics?
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
What is KEGG pathway enrichment?
KEGG mapping is the process to map molecular objects (genes, proteins, small molecules, etc.) to molecular interaction/reaction/relation networks (KEGG pathway maps, BRITE hierarchies and KEGG modules). It is not simply an enrichment process; rather it is a set operation to generate a new set. pathway mapping.
What is meant by Gene Ontology?
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. Whereas gene nomenclature focuses on gene and gene products, the Gene Ontology focuses on the function of the genes and gene products.
How do you get the gene list from the KEGG pathway?
you can download list of pathway an the genes for humans http://rest.kegg.jp/link/hsa/pathway . You can use excel or sql or any language of your choice, to group the list based on unique pathway and a grouped comma or space separated list of genes. If this is what you need can make that file and share.
What is a KEGG category?
KEGG is an integrated database resource consisting of sixteen databases shown below. They are broadly categorized into systems information, genomic information, chemical information and health information, which are distinguished by color coding of web pages. Category.
How many KEGG pathways are there?
Current Statistics
| KEGG Database as of 2021/12/23 | ||
|---|---|---|
| KEGG PATHWAY | Pathway maps, reference (total) | 548 (856,927) |
| KEGG BRITE | Functional hierarchies, reference (total) | 180 (298,427) |
| KEGG MODULE | KEGG modules Reaction modules | 456 46 |
| Genomic information |
What are KEGG modules?
KEGG modules are defined as characteristic gene sets that can be linked to specific metabolic capacities and other phenotypic features, so that they can be used for automatic interpretation of genome and metagenome data. Another database that supplements KEGG PATHWAY is the KEGG BRITE database.
What is KEGG Orthology?
The KO (KEGG Orthology) database is a database of molecular functions represented in terms of functional orthologs. A functional ortholog is manually defined in the context of KEGG molecular networks, namely, KEGG pathway maps, BRITE hierarchies and KEGG modules.
WHAT IS A GO classification?
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.
How are Gene Ontology terms arranged?
GO is subdivided into three non-overlapping ontologies: Molecular Function (MF), Biological Process (BP) and Cellular Component (CC). The structure of GO is a Directed Acyclic Graph (DAG), where the terms are the nodes and the relations among terms are the edges.
What is Ko (KEGG ORTHOLOGY)?
Molecular functions are stored in the KO (KEGG Orthology) database containing orthologs of experimentally characterized genes/proteins. Genome annotation in KEGG is to assign KO identifiers (or K numbers) to individual genes in the genome.
What is K number in KEGG pathway?
Each node of the network, such as a box in the KEGG pathway map, is given a KO identifier (called K number) as a functional ortholog defined from experimentally characterized genes and proteins in specific organisms, which are then used to assign orthologous genes in other organisms based on sequence similarity.
What is genome annotation in KEGG?
Genome annotation in KEGG is to assign KO identifiers (or K numbers) to individual genes in the genome, rather than giving text description of functions.
How many top categories are there for KEGG pathway maps?
It consists of six top categories (09100 to 09160) for KEGG pathway maps and one top category (09180) for BRITE hierarchies, as well as one top category (09190) for those KOs that are not yet included in either of them.
