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NCI-Nature Pathway Interaction Database; Netpath: curated resource of signal transduction pathways in humans; 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 ...
Such a pathway can trigger the assembly of new molecules, such as a fat or protein. Pathways can also turn genes on and off, or spur a cell to move. [1] Some of the most common biological pathways are involved in metabolism, the regulation of gene expression and the transmission of signals. Pathways play a key role in advanced studies of genomics.
Toolkit to address many common challenges at biological databases Unix-like (server), Web browser (client) Varies depending on tool Collaborative project GenGIS: Application that allows combining digital map data with information about biological sequences collected from the environment Windows, macOS: GPL: Collaborative project GenoCAD
Examples of biological pathways in Reactome include signal transduction, innate and acquired immune function, transcriptional regulation, programmed cell death and classical intermediary metabolism. The pathways represented in Reactome are species-specific, with each pathway step supported by literature citations that contain an experimental ...
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.
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.
Based on the manual curation done, BioCyc database family is divided into 3 tiers: Tier 1: Databases which have received at least one year of literature based manual curation. Currently there are seven databases in Tier 1. Out of the seven, MetaCyc is a major database that contains almost 2500 metabolic pathways from many organisms.
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).