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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