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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.
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 ...
KEGG PATHWAY Database (Univ. of Kyoto) MANET database (University of Illinois) Reactome: navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling (Ontario Institute for Cancer Research, European Bioinformatics Institute, NYU Langone Medical Center, Cold Spring Harbor Laboratory)
Schematic overview of the modular structure underlying procedures for gene set enrichment analysis. Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with different phenotypes (e.g ...
Pathway Enrichment Analysis (which is similar to MSEA) identifies which metabolic pathways have compounds (from the input lists) that are over-represented and have significant perturbations to their concentrations. MetPA uses a number of robust statistical measures to identify which metabolites (and therefore which pathways) are over-represented.
FunRichFunctional Enrichment analysis tool. GAGE is applicable independent of sample sizes, experimental design, assay platforms, and other types of heterogeneity. [148] This Biocondutor package also provides functions and data for pathway, GO and gene set analysis in general.
The KEGG pathway map of Rickettsia rickettsii is visualised by GLAMM with a metabolite highlighted. The Pathway Browser lets users to navigate the Kyoto Encyclopedia of Genes and Genomes (KEGG) [11] pathway maps displaying predicted presence or absence of enzymes for up to two selected genomes. The map of a particular pathway and a comparison ...
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.