Table 1 A description of the reaction types processed by Sig2BioPAX
From: Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format
| Reaction Type | Description |
|---|---|
| Binding | Molecules bind to form a complex |
| Kinase Phosphorylation | Kinase catalyzes addition of phosphate group to target molecule |
| Dephosphorylation | Catalyst initiates removal of phosphate group from target molecule |
| Guanine Nucleotide Exchange | GDP removed from complex and replaced with GTP |
| GTPase activating protein | GTP bound to compound becomes GDP |
| Ubiquitination | Ubiquitin molecule is added to target compound |
| Deubiquitination | Ubiquitin molecule is removed from target compound |
| Sumoylation | Small ubiquitin-related modifier is attached to target molecule |
| Cleavage with Phospholipase C | PLC cleaves PIP2 into IP3 and DAG |
| Cleavage on Cysteine | Deactivating cleavage on a cysteine residue of target protein |
| Inactivating Cleavage | Deactivating cleavage of target molecule |
| Activating Cleavage | Cleavage of pro-protein into active form |
| Protein-protein Interaction | Otherwise unspecified reaction between two proteins |
| Transcription | Protein activates or inhibits transcription of gene products |
| Transcription Factor Promoter Binding | Transcription factor and protein bind to create complex |