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A reconstruction breaks down metabolic pathways (such as glycolysis and the citric acid cycle) into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances.KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
As such, these networks comprise the chemical reactions of metabolism, the metabolic pathways, as well as the regulatory interactions that guide these reactions. With the sequencing of complete genomes , it is now possible to reconstruct the network of biochemical reactions in many organisms, from bacteria to human.
The KEGG resource [109] provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES), the chemical space (KEGG LIGAND), wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY), and ontologies for pathway reconstruction (BRITE database). [110]
Pathway resources and types of pathway analysis using databases like KEGG, Reactome and WikiPathways. [1]Pathway is the term from molecular biology for a curated schematic representation of a well characterized segment of the molecular physiological machinery, such as a metabolic pathway describing an enzymatic process within a cell or tissue or a signaling pathway model representing a ...
Central or highly important metabolites are “hubs”, located in the center of a metabolic pathway or process. MetPA employs a number of topological assessment tools to measure centrality or “hubness” in an objective manner (called Pathway Impact). Pathway impact is a combination of the centrality and pathway enrichment results.
Following annotation, KEGG (Kyoto Encyclopedia of Genes and Genomes) enables visualization of metabolic pathways and molecular interaction networks captured in the transcriptome. [ 13 ] In addition to being annotated for GO terms, contigs can also be screened for open reading frames (ORFs) in order to predict the amino acid sequence of proteins ...
KEGG Pathway database is a popular pathway search database highly used by biologists. WikiPathways is a community curated pathway database using the "wiki" concept. All pathways have an open license and can be freely used. Reactome is a free and manually curated online database of biological pathways.