PHI-Canto v1509
Community curation
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Curating Physical Interactions

If you have physical interactions to curate, please read the Directionality section carefully.

We recommend that you only annotate interactions that you think are biologically meaningful. For example, don't include known or suspected contaminants from mass spectrometry results (e.g. ribosomal proteins, translation factors, 'sticky' proteins).

When you choose 'Physical interaction', a popup appears with two pulldown menus and a text field for optional comments.

Choose an evidence type from the first pulldown menu. Some evidence types have a brief description that indicates the directionality. Further information on evidence supporting genetic interactions is available an the BioGRID help wiki and in the Directionality section below.

Choose the interacting gene from the second pulldown menu. Click 'OK' to finish the annotation and close the popup.

Note that only pairwise genetic interactions can be annotated in Canto.

Directionality

Some experiments that detect physical interactions have an inherent directionality. For example, in a typical two-hybrid experiment one protein (A) is fused to a DNA binding domain and a second (B) is fused to a transcription activation domain. The reciprocal experiment, with A fused to the activation domain and B fused to the DNA binding domain, may or may not have been done.

For such "asymmetric" interactions, Canto allows you to curate in only one direction starting from the gene you have selected, as indicated in the evidence selector.

If the evidence description looks the wrong way around, you will have to change genes and start again. (You can finish and then delete an interaction annotation if you find that you have started with the wrong gene.)

Evidence Relationship between Interactor A (bait) and Interactor B (prey)
Affinity Capture-Luminescence affinity captures
Affinity Capture-MS affinity captures
Affinity Capture-RNA affinity captures
Affinity Capture-Western affinity captures
Far Western captures
FRET fluorescence resonance energy donor to
Protein-peptide binds to peptide
Protein-RNA binds to RNA
Two-hybrid binds activation domain construct with
Use one of the Affinity Capture evidence types for co-immunoprecipitation. If you have done the experiment in both directions, you should curate two annotations to describe the interaction completely. Curate starting from one gene, then switch genes to annotate the reciprocal experiment. Other experiment types are "symmetric" and therefore only need to be entered once, and you can start from either of the interacting genes.
Evidence Relationship between gene A and gene B products
Co-crystal Structure co-crystallizes with
Co-fractionation co-fractionates with
Co-purification co-purifies with
Reconstituted Complex forms complex with
PCA* interacts with
*Note that PCA is not exactly symmetric, since there will be one N-terminal and one C-terminal reporter fusion construct, but it is treated as symmetric in Canto.