Details about TRANSPATH Chains and Pathways

Pathway Reports contain two types of entities: pathways and chains. Pathways reflect canonical pathways for specific signaling molecules (mostly ligands or receptors) and are made up of one or more chains. Chains are sets of consequent reactions; in other words, the reactions contain common molecules. Chains that are linked to pathways consist of reactions of the type "pathway step". Chains can have bifurcations and even loops that carry regulatory meaning. Figure 1 shows how pathways and chains are connected to the reaction hierarchy.

Figure 1. Pathways and Chains in the Reaction Hierarchy

The construction of chains and pathways is based on recent (primary and review) literature and on the expert knowledge of the curator who has worked intensely on the specific topic. In some cases, when a sequence of reactions has been reported by one primary paper, the chain is labelled as an evidence chain. We assume that the physiological relevance of a reaction sequence is higher when one group has proved it in a consistent experimental system.

Chains that are constructed from metabolic pathway step reactions are referred to as metabolic chains. Metabolic pathway and chain data in TRANSPATH reflect the canonical metabolic pathway knowledge from most recent textbooks.