Table 2

List of predefined interaction types

Interaction type

Gene

Ligand


Acts on upstream signaling pathway

Competitive inhibition

Genetic

Indirect

Multimerization

Not specified

Physical: deacetylation

Physical: dephosphorylation

Physical: desumoylation

Physical: deubiqiutination

Physical: enzyme modification: acetylation

Physical: enzyme modification: methylation

Physical: enzyme modification: phosphorylation

Physical: enzyme modification: protein cleavage

Physical: enzyme modification: sumoylation

Physical: indirect altering posttranslational modifications

Physical: sequestering

Physical: translocation

Physical: ubiquitination

Physical: undefined direct interaction

Physical: with another TF

Physical: with another TF: complex binds DNA

Physical: with co-activator affecting recruitment

Physical: with co-repressor affecting recruitment

Regulatory: decreases expression of this TF

Regulatory: increases expression of this TF

Unknown


When a protein-to-protein or protein-to-ligand is added to a TFe article either by the author or automatically from BioGRID, the author of that article has the option to define the interaction type if this information is known. To promote a standardized vocabulary for describing interaction types, a list of possible interaction types between proteins and ligands is provided to the author. This list continues to be adjusted and expanded based on need and author feedback.

Yusuf et al. Genome Biology 2012 13:R24   doi:10.1186/gb-2012-13-3-r24

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