A biological pathway is a series of interactions among molecules in a cell that leads to a certain product or a change in a cell. 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. 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.
Most common types of biological pathways:
- 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.
- 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).
- PhosphoSitePlus is a database of observed post-translational modifications in human and mouse proteins; an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, ubiquitination, acetylation and methylation.
- BioCyc database collection is an assortment of organism specific Pathway/Genome Databases.
- Human Protein Reference Database is a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome (the last release was #9 in 2010).
- PANTHER (Protein ANalysis THrough Evolutionary Relationships) is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products.
- TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles (provided by geneXplain GmbH).
- MiRTarBase is a curated database of MicroRNA-Target Interactions.
- DrugBank is a comprehensive, high-quality, freely accessible, online database containing information on drugs and drug targets.
- esyN is a network viewer and builder that allows to import pathways from the biomodels database or from biogrid, flybase pombase and see what drugs interact with the proteins in your network.
- Comparative Toxicogenomics Database (CTD) is a public website and research tool that curates scientific data describing relationships between chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, GO annotations, pathways, and interaction modules; CTD illuminates how environmental chemicals affect human health.
- Pathway commons is a project and database that uses BioPAX language to convert, integrate and query other biological pathway and interaction databases.