Pathway-Network Databases

  • • KEGG58 KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. The KEGG home page has links to several data-oriented entries including: KEGG pathway maps, BRITE functional hierarchies, KEGG modules, ortholog groups, genomes, genes and proteins, small molecules, glycans, biochemical reactions, enzymes, human diseases, drugs, and health information resources. There are also several analytical tools including mapping tools, pathogen checker of antimicrobial resistance genes, sequence similarity search, and chemical similarity search. The KEGG is a primary source of information for most databases that include pathway information.
  • Reactome59 Reactome is a curated and peer-reviewed pathway database that provides intuitive bioinformatics tools for visualization, interpretation, and analysis of pathway knowledge. Data mining and analysis tools include a pathway browser, tools that merge information into a portal, species comparisons, cystoscope plug-in, small molecule search, and literature citation searching.
  • Cytoscape60 Software platform for visualizing molecular interaction networks and biological pathways. Networks can be integrated with annotations, gene expression profiles, and other data. Additional features include apps, formerly called plug-ins (mostly free) which allow network and molecular profiling, different layouts, and connection with databases. Cytoscape links are frequently available with several other databases.
  • Pathway Commons61 pathway Commons stores and disseminates knowledge about biological pathways: >42 000 pathways and 1 350 000 interactions from 22 data sources.
  • NDEx62 The network Data Exchange provides an open-source framework where scientists and organizations can share, store, manipulate, and publish biological network knowledge.
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