FAQs
Phenotype annotations¶
How do I indicate that a mutation or deletion is viable?¶
Annotate a genotype including that allele to viable vegetative cell population. Viability can depend on conditions and other alleles present on the genotype. See phenotypes
How do I indicate that a mutation or deletion is lethal?¶
Annotate a genotype including that allele to inviable vegetative cell population. Lethality can depend on conditions and other alleles present on the genotype. See phenotypes
How do I indicate that an allele is thermosensitive?¶
Annotate a genotype including that allele to inviable vegetative cell population, including high temperature or low temperature as a condition. See phenotypes
Genotype management¶
What's the difference between "Wild type product level" and "Not assayed"?¶
Historically, Wild type product level and Not assayed have been used interchangeably when a non-wild type allele is expressed from the endogenous locus. We recommend Not assayed if you have not measured expression. See Genotype management
What to do when control strains over-express the wild-type allele, or express it from a plasmid?¶
PomBase does not capture the difference between strains expressing an allele from a plasmid or the native locus in phenotype annotations. Similarly, we do not have a way to capture the fact that the control of an experiments is over-expressing the wild-type allele. Therefore, if both the wild-type (control) and mutant allele are over-expressed / knocked-down, the meaning in Expression is ambiguous. If you think the expression level plays a role in producing the phenotype, select Overexpression or Knockdown. Otherwise, select Not assayed. See Genotype management
What if the wild-type copy is still present in a mutant strain?¶
Multi-loci phenotype can be used to indicate that the wild-type allele is still present in a strain expressing an allele of that gene. For example, a strain that bears both the wild type cdc25 and the mutant allele cdc25-22. For this purpose, you can create a wild-type allele with expression level Wild type product level. See Genotype management
Genetic interactions¶
How do I annotate positive or negative genetic interactions?¶
Positive and negative interactions are only allowed by BioGrid for high-throughput studies, so they cannot be added in Canto. * If you want to submit a high-throughput dataset of genetic interactions, you can do so in BioGrid, and it will appear in PomBase. * Otherwise, visit PomBase genetic interaction documentation, to find what type of genetic interaction fits your case.
How do I annotate a rescue?¶
Rescues can correspond to different types of genetic interactions depending on the genotypes and phenotypes involved, visit PomBase genetic interaction documentation, to find what type of genetic interaction fits your case.
Physical interactions¶
Does the order of genes in physical interaction matters.¶
In most cases, it does. Visit the physical interaction page
Other¶
Can I submit high-throughput datasets?¶
Yes, but not through Canto. See PomBase Data Submission.
I have spotted an error, what can I do?¶
If you are familiar with GitHub, you can propose a fix yourself by clicking on the link at the top-right of
every page that says Found a mistake? Fix it in on GitHub!. Alternatively, send us an email.
Can I contribute to these guidelines?¶
If you are familiar with GitHub, you can create a pull request at the repository: https://github.com/pombase/canto_tutorial
Alternatively, send us an email.
Any contribution is welcome, including FAQs and extra documentation.