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PomBase curation
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publications for interaction interface Canto testing #2675

Open mah11 opened 4 years ago

mah11 commented 4 years ago

PMID:32204793 https://github.com/pombase/curation/issues/2675 from author:

"The sfr1 deletion mutant is sensitive to DNA damage by itself, and this sensitivity is enhanced by deletion of rad55 or rad57. By contrast, the amino acid substitution mutants do not show any DNA damage sensitivity by themselves. However, in the absence of rad55 or rad57, they do show a synergistic negative interaction."

also see helpdesk ticket 7670

mah11 commented 4 years ago

could also upgrade the interactions in PMID:32341083

ValWood commented 4 years ago

PMID:32053662 there is a genetic interaction between Ssp2 and Gsk3/Gsk31, and Ssp2 and Gsk3/Gsk31 may act on parallel pathway in regulation of Sre1 activity

ValWood commented 4 years ago

from https://github.com/pombase/curation/issues/2540

Genetic interactions of dmfl with other genes required for septation Strains carrying either the dmfl-6 or dmfl ::ura4+alleles were crossed to strains carrying either cdc3-6, cdc4-8, cdc7-24, cdc8-110, cdc11-136, cdc12-112, cdc14-118, cdcl 5-140, or cdcl 6-116. The null allele is synthetically lethal with cdc4-8 and cdc3-6, and the restrictive tem- perature of double mutants with cdc7-24 and cdc15-140 was reduced to 25~ Double mutants with dmfl-6 showed less severe effects, but dmfl-6 cdc4-8, dmfl-6 cdc7-24, and dmfl-6 cdc15-140 all have a reduced non- permissive temperature compared with the single mutants.

mid1 paper is https://www.pombase.org/reference/PMID:8946912

MariaSanta's paper is https://www.pombase.org/reference/PMID:31509478

ValWood commented 3 years ago

This paper illustrates why we really need to be able to use "suppression" and "enhancement" with specific genotypes and phenotypes.

The single mutants are already "high expressivity" but subsequent additions enhance the phenotype more and we run out of "expressivity". we need really high and really really high!

In this session I adjusted to low, medium, high but this isn't ideal when you have subtle enhancements. It will be so much better when we can do this in the GI interface and select genotype A phenotype Y enhanced by genotype B....

supressors and enhancers

from https://github.com/pombase/curation/issues/2432

ValWood commented 3 years ago

22 supressors in PMID:34028542 where ther author has nicely included the alleles and phenotypes in the comment

ValWood commented 3 years ago

PMID:34279633 imp1/cdc15 double mutants would be good GI interface candidates (not curated in test)

mah11 commented 3 years ago

PMID:34292936 different alleles of pcn1 have opposite effects on rad51delta GRC rate

ValWood commented 2 years ago

PMID:33534698 I can't reconcile this:

Screenshot 2022-08-24 at 13 32 55 Screenshot 2022-08-24 at 13 34 11

====

PMID:34738170 [Kaoru Takegawa] session in approval

ValWood commented 2 years ago

https://www.pombase.org/reference/PMID:34389684 (author recorded the alleles in the GI section)

ValWood commented 2 years ago

https://www.pombase.org/reference/PMID:34958661 (session not in test)

ValWood commented 2 years ago

PMID:15546915 GI->phenotype connection recorded in comments partially suppresses hypersensitivity to Cal- cofluor (Cfw) and Echinocandin (Ech) but does not rescue lysis at 37°C in the ehs2-1 mutant (Tajadura et al., 2004).

https://github.com/pombase/canto/issues/2611

ValWood commented 1 year ago

author recorded phenotype

PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 formaldehyde sensitivity PMID:32034465 camptothecin sensitivity PMID:32034465 camptothecin sensitivity PMID:32034465 formaldehyde sensitivity

ValWood commented 1 year ago

PMID:24239120 Fig. S1 (This is a rescue of FYPO:0000324) PMID:24239120 Fig. S1 (This is a rescue of FYPO:0000324) PMID:24239120 Fig. S1 (This is a partial rescue of FYPO:0004307) PMID:24239120 (This is a rescue of FYPO:0000324) PMID:24239120 (This is a rescue of FYPO:0000324) PMID:24239120 (This is a partial rescue of FYPO:0004307) PMID:24239120 Fig. 2 (This is a rescue of FYPO:0004395) PMID:24239120 Fig. 2 (This is a rescue of FYPO:0004395) PMID:24239120 (This is a rescue of FYPO:0004395 and FYPO:0004101 partially) PMID:24239120 (This is a rescue of FYPO:0004395) PMID:24239120 Fig. 2 (This is a rescue of FYPO:0000324) PMID:24239120 (This is a rescue of FYPO:0000324)