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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 ...
The website can be used to browse pathways and submit data to a suite of data analysis tools. The underlying data is fully downloadable in a number of standard formats including PDF, SBML, Neo4j GraphDB, MySQL, PSI-MITAB, and BioPAX. Pathway diagrams use a Process Description (PD) Systems Biology Graphical Notation -based style.
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.
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)
WikiPathways is originally built using MediaWiki software, [4] a custom graphical pathway editing tool (PathVisio [5]) and integrated BridgeDb [6] databases covering major gene, protein, and metabolite systems. WikiPathways was founded in 2008 by Thomas Kelder, Alex Pico, Martijn Van Iersel, Kristina Hanspers, Bruce Conklin and Chris Evelo.
PathwaySeq [154] Pathway analysis for RNA-Seq data using a score-based approach. petal Co-expression network modelling in R. ToPASeq: [155] an R package for topology-based pathway analysis of microarray and RNA-Seq data. RNA-Enrich A cut-off free functional enrichment testing method for RNA-seq with improved detection power.
Using the web-interface of the database, one can perform overrepresentation analysis, based on biochemical pathways or on neighbourhood-based entity sets (NESTs) that constitute sub-networks of the overall interaction network containing all physical entities around a central one within a "radius" (number of interactions from the center).
All pathways have an open license and can be freely used. Reactome is a free and manually curated online database of biological pathways. NCI-Nature Pathway Interaction Database is a free biomedical database of human cellular signaling pathways (new official name: NCI Nature Pathway Interaction Database: Pathway, synonym: PID).