How BioGRID's notation maps to what we want to display in PomBase web pages
Interactor A = subject (in chado) = "bait"
Interactor B = object (chado) = "hit" or "prey"
Also see BiogridSymmetry
BioGRID evidence | Symmetric? | Interactor A (bait, subject) | Interactor B (hit, prey, object) |
Co-crystal Structure | Y | co-crystallizes with | co-crystallizes with |
Co-fractionation | Y | co-fractionates with | co-fractionates with |
Co-localization (not used by PomBase) | Y | n/a (would be co-localizes with) | n/a (would be co-localizes with) |
Co-purification | Y | co-purifies with | co-purifies with |
Reconstituted Complex | Y | forms complex with | forms complex with |
Affinity Capture-Luminescence | N | affinity captures | affinity captured by |
Affinity Capture-MS | N | affinity captures | affinity captured by |
Affinity Capture-RNA | N | affinity captures | affinity captured by |
Affinity Capture-Western | N | affinity captures | affinity captured by |
Biochemical Activity (not used by PomBase) | N | n/a (would be modifies) | (would be modified by) |
Far Western | N | captures | captured by |
FRET | N | fluorescence resonance energy donor to | fluorescence resonance energy acceptor from |
PCA | N* | interacts with | interacts with |
Protein-peptide | N | binds to peptide | (peptide) binds to protein |
Protein-RNA | N | binds to RNA | binds to protein |
Two-hybrid | N | binds activation domain construct with | binds DNA-binding domain construct with |
Negative Genetic | Y | negative genetic interaction with | negative genetic interaction with |
Positive Genetic | Y | positive genetic interaction with | positive genetic interaction with |
Synthetic Growth Defect | Y | synthetic growth defect with | synthetic growth defect with |
Synthetic Haploinsufficiency | Y | synthetic haploinsufficient with | synthetic haploinsufficient with |
Synthetic Lethality | Y | synthetic lethal with | synthetic lethal with |
Synthetic Rescue | N | synthetically rescued by | synthetically rescues |
Dosage Growth Defect | N | growth defect in presence of overexpressed | overexpression causes growth defect to |
Dosage Lethality | N | inviable in presence of overexpressed | overexpression lethal to |
Dosage Rescue | N | rescued by overexpression of | overexpression rescues |
Phenotypic Enhancement | N | phenotype enhanced by | enhances phenotype of |
Phenotypic Suppression | N | rescued by | rescues |
- PCA is not exactly symmetric, since there will be one N-terminal and one C-terminal reporter fusion construct, but we're not going to capture that. PCA can therefore be handled the same way as the symmetric interactions in the curation tool.
Last modified 9 years ago
Last modified on Apr 17, 2012, 4:12:26 PM