Provides a list of convention for annotating and organize relationships in bioregulatory systems. MIM notation describes the relationships between multiple entities by using interactions glyphs, a controlled vocabulary and typographical convention. The system is able to display complex set of regulatory network interconnections or to capture different cell types and cell states. It also allows the specification of known molecular data as well as the addition of contingencies.
A wiki-based visual encyclopedia of aging processes that will facilitate rapid exploration of aging pathways and mechanisms by experts and entrants to the field alike. Building on an initial content base constructed by a team of experts from peer-reviewed literature, users can integrate new data into biological pathway diagrams for a visible, intuitive, top-down framework of aging processes that fosters knowledge-building and collaboration. Aging Chart is an extension of the community curation model for pathway collections and is the first such resource to serve the growing community of researchers interested in the cellular and molecular biology of aging.
Contains cellular events in humans, mice, and rats, collected from over 31,500 publications. Transpath offers information about the intracellular signaling pathways. It allows the user to see details of the signal flow from the cell surface into the nucleus, focusing on mammals such as humans, mice, and rats. The database is organized by genes/molecules and by reactions according to multiple hierarchies and is manually curated.
An annotated database of signaling cascades. PathDIP integrates data from 20 source pathway databases, comprising core pathways from major curated pathways databases, and extended pathways predicted by using physical protein interactions. Data integration and predictions increase coverage of pathway annotations for protein-coding genes to 86%, and provide novel annotations for 5,732 pathway orphans. PathDIP annotates 17,070 protein-coding genes with 4,678 pathways, and provides multiple query, analysis and output options.
A comprehensive database resource for systems biology of DNA damage and repair. REPAIRtoire collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair and (iv) diseases correlated with mutations in genes encoding DNA repair proteins. Pathways are represented as graphs and in tabular form with descriptions of each repair step and corresponding proteins, and individual entries are cross-referenced to supporting literature and primary databases. REPAIRtoire can be queried by the name of pathway, protein, enzymatic complex, damage and disease.
An integrated dataset of human pathways and protein-protein interactions. We developed a series of rules for transforming protein interactions from pathway to binary model, and the protein interactions from seven pathway databases, including PID, BioCarta, Reactome, NetPath, INOH, SPIKE and KEGG, were transformed based on these rules. These pathway-derived binary protein interactions were integrated with PPIs from other five PPI databases including HPRD, IntAct, BioGRID, MINT and DIP.
Gathers information about receptor activator of nuclear factor-kappa B ligand (RANKL) and Receptor activator of nuclear factor-kappa B (RANK) stimulated reactions. RANKL Signaling Pathway is a manually curated database providing data about protein–protein interactions (PPIs), enzyme–substrate reactions or protein translocation events. Searches can be made by gene symbol, protein name, accession number or pathway name.