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.

Cytoscape pathway analysis