Inferred from Physical Interaction (IPI)
IPI: Inferred from Physical Interaction
- 2-hybrid interactions
- Ion/protein binding experiments
Covers physical interactions between the entity of interest and another molecule (such as a protein, ion or complex). IPI can be thought of as a type of IDA, where the actual binding partner or target can be specified, using "with" in the with/from field.
Often it is difficult to tell from the evidence presented in a paper whether an interaction is direct or not. Any in vivo/cell lysate method always has the possibility of a third 'bridge' protein - there are many examples of this happening in, for example, yeast 2-hybrid experiments when yeast proteins have proven essential for interactions between two human proteins to occur. The only methods that show direct evidence of two proteins binding are when the two proteins have been isolated and pre-purified. Ideally, curators should only capture direct interactions however, it is acceptable to curate interactions even if it is not known whether they are direct or not.
Examples where the IPI evidence code should be used:
- Binding assays where it is possible to put an ID corresponding to the specific binding partner that was shown to interact with the entity being annotated should be annotated with the IPI code, not with IDA.
- Annotations to the GO term ‘binding’ (GO:0005488) or ‘protein complex' (GO:0043234), or their child terms, which are supported by the isolation of a complex by co-immunoprecipitation or pull-down assays may use IPI with the ID corresponding to the ‘antibody target' or ‘tagged' subunit in the with/from column.
- The GO term ‘protein binding’ (GO:0005515) should only be used with the evidence code IPI and an identifier in the ‘with’ field. A reciprocal annotation must also be made to indicate the interaction in the opposite direction.
- Annotations to Molecular Functions (except ‘catalytic activity’ GO:0003824 or its child terms, see below) or Biological Processes may be made using IPI and an entry in the ‘with/from’ field in order to indicate the inference that the annotated entity is involved in the process or function because it interacts with another entity that was shown experimentally to be involved in that process or function.
Examples where the IPI evidence code should not be used:
- The GO term ‘protein binding’ (GO:0005515) should not be used to describe an antibody binding to another protein. However, an effect of an antibody on an activity or process can support a function or process annotation, using the IMP code.
- Annotations to the GO term ‘binding’ (GO:0005488), or its child terms, which are supported by binding assays where it is NOT possible to put an ID corresponding to the specific binding partner that was shown to interact with the gene product being annotated should be annotated with the IDA code, not with IPI (see table 1).
- Annotations to the GO term ‘catalytic activity’ (GO:0003824), or its child terms, should not use the IPI evidence code. It is unlikely that enough information can be obtained from a binding interaction to support such an annotation.
Table 1. Example annotation where it is not possible to add the interacting partner.
|DB Object ID||DB Object Symbol||GO ID||DB:Reference||Evidence Code||With (or) From|
|MGI:2137706||Actn1||GO:0051015 (actin filament binding)||PMID:15465019||IDA||-|