Here are the instructions for adding phenotypes to genetic interactions using the experimental systems and the 'observables' from the Yeast Phenotype Ontology (YPO). Please note that the YPO is still evolving, and if we come across missing terms we can request them by sending an email to SGD (pheno-curator@genome.stanford.edu). Selecting a genetic interaction type will open up tree display of SGD's observable ontology in the lower left corner of the curator form. Clicking on the text 'SGD Observable Ontology' will expand the ontology.
The default phenotype for all of these is 'inviable' or 'vegetative growth', as appropriate. However, we have also decided to add a secondary phenotype using the observables ontology, if applicable. Therefore, the synthetic lethal or growth defect interactions would be curated as follows:
Note that for any temperature sensitive phenotype, 'heat sensitivity' or 'cold sensitivity' can be selected under the Cellular Processes → Stress Resistance → Temperature Sensitive Growth section of the YPO.
Here are some examples from Fig. 2 in PMID 17951629:
The pem1 pem2 double mutant is a choline auxotroph and thus needs choline or lyso-phosphotidylcholine to grow. If you delete lem3 in this background, the strain can no longer grow with lyso-phosphotidylcholine.
bait = pem1
hit = pem2
interaction = synthetic growth defect
(default phenotype = vegetative growth)
curated secondary phenotype = auxotrophy
qualification = pem1 pem2 double mutants are choline auxotrophs and need choline or lyso-phosphotidylcholine to grow.
baits= pem1 pem2
hit = lem3
interaction = synthetic growth defect
(default phenotype = vegetative growth)
curated secondary phenotype = nutrient uptake (according to results discussed by authors, but could also select 'nutrient utilization')
qualification = pem1 pem2 double mutants are choline auxotrophs and need choline or lyso-phosphotidylcholine to grow. If lem3 is deleted in this background, the strain can no longer grow with lyso-phosphotidylcholine.
We will also curate certain chemical genetic interactions and haploinsufficiency interactions using the following experimental systems, as appropriate:
Chemical genetic interactions: we will only curate some types of chemical-genetic screens that involve interactions. For example, the experiment in PMID 17923092 essentially represents a synthetic genetic analysis using a small-molecule inhibitor to inhibit Hsp90 function (the specific Hsp90-inhibiting drug macbecin II (MII)), instead of an actual hsp90 (hsp82/hsc82) mutation. They also used some arrays to identify the interacting genes. For now we will curate these types of interactions using the synthetic lethality/growth defect tag and will add a qualification noting that it's a chemical genetic experiment and the chemical used in the study. An additional experimental system called “chemical genetic” may be added to the IMS system at a later date. Please note that we will not be curating typical chemical genetic studies where they screen a collection of single mutants using chemicals because they do not involve any interactions (e.g. see PMID 18420932).
Haploinsufficiency interactions: an example would be double heterozygous mutants such as YFG1/yfg1-delta yfg2-delta/YFG2 strains that result in sickness or lethality (e.g.see PMID 17167106). We will curate them using the 'synthetic haploinsufficiency' tag and note the phenotype 'haploinsufficient' under the 'fitness' term in the phenotype drop-down menu.
Select the phenotype(s) being enhanced from the observables ontology on the IMS page (as many as appropriate). For example:
Select the phenotype(s) being suppressed or rescued from the drop down menu on the IMS page (as many as appropriate), i.e. the phenotype of the bait single mutant. For any temperature sensitive phenotype, 'heat sensitivity' or 'cold sensitivity' can be selected under the Cellular Processes → Stress Resistance → Temperature Sensitive Growth section of the YPO. Using the pull-down menu on the bottom right of the curator form, add the final phenotype of the double mutant as either (a) wild type, (b) partial rescue or © undetermined.
If you have the same interaction (i.e. bait/prey and experimental system) with more than one phenotype but different levels of suppression/rescue, then enter the interaction twice. For example:
We will continue to curate triple mutants by choosing a bait and hit and entering a note in the qualification field to indicate that it's a triple mutant. For example, in PMID 19136626, there's a synthetic growth defect due to an interaction between srs2 and mph1, and also a synthetic rescue experiment that shows the triple mutant srs2 mph1 rad51 has normal growth. For this case, we curate the synthetic growth defect interaction between srs2 and mph1, then curate srs2-rad51 and mph1-rad51 as synthetic rescue, with a note that it's a triple mutant.
We will continue to do this even for triple mutants that only show a phenotype when all the genes are mutated. For example, in PMID 19339687 (Fig. 2) there's a triple mutant that is synthetic lethal but mutation in any two of the three genes has no phenotype. There are three genes involved and the interactions should be entered as A-B, B-C and C-A with a note in the qualification box that it is a triple mutant, and the name of the third gene.
Note that there are several triple mutants in BioGRID that are confusing for users because the qualifications are not yet being displayed (although they are displayed in SGD). We will sort through these triple mutants at a later date and improve their display.