WikiPathways offers a good selection of organisms. WikiPathways works under the same principles: users can contribute to the open-source pathway resource by suggesting new pathways to be added or by creating novel pathways. PANTHER pathway, however, encourages user-curation and user-creation of novel pathways. PANTHER pathway is a rather small resource, with currently 176 primarily signaling pathways. BioCyc has a large collections of metabolic and regulatory pathways for ~5,500 organisms, with components such as EcoCyc and MetaCyc, 6 or HumanCyc. Reactome has pathways for a selected number of organisms, representing mostly the commonly used model organisms. It is to our knowledge the largest pathway resource, with metabolic and signaling pathways from a pleiotropy of organisms. The KEGG pathway database was first published in the year 1997 and has since been updated regularly. ![]() ![]() Many different studies are collected and integrated over time by initiatives like KEGG, 1 Reactome, 2 PANTHER pathway, 3 BioCyc, 4 or the user-curated WikiPathways 5 ( Table 1). Pathways come in different flavors, depending on their functions in the cell – the three main types are metabolic pathways, gene regulatory pathways, and signaling pathways.īiological pathways are generally derived from experimental work in cell culture or model organisms. Activation of a pathway typically leads to a change of state in the cell: as examples, a set of genes is transcribed, new molecules are assembled, molecules are secreted, or new signals are recognized. The study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions.
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