#782 allow wild type endogenous or not specified in genotype

[Midori Harris]

transferred from wiki

I think it was part of the original multi-gene phenotype spec that for genotypes that have both a wild-type copy and a mutant copy of the same gene, either or both can be at the endogenous expression level (if not, it should've been). So we need this change in the interface:

Allow a wild type allele at endogenous or "not specified" expression as part of a genotype. The single gene phenotype version should not change -- that should still only offer overexpression and knockdown for wild type. If possible, it would be nice to have a warning if a genotype only has wild type, endogenous expression (and no other alleles) for any one gene.

[Valerie Wood]

Kim might need to talk to Midori about this one. We think it is important enough to go at "8" but aren't quite sure what is required.

[Kim Rutherford]

Is this a good summary?:
A wild type allele can only have endogenous expression if there is another copy of the same gene in the genotype

I guess things are different for diploid organisms?

[Midori Harris]

Is this a good summary?

It is indeed.

I guess things are different for diploid organisms?

Yes, this ticket has been mainly about haploids where someone has stuffed in more than one copy of just one gene of interest (or maybe up to a few genes).

Diploids should have two copies of every gene, with the inevitable exceptions when people go to study the effects of having one copy of a gene-of-interest in an otherwise diploid organism ...

The genotype stuff in the database and the Canto genotype-specifying interface should handle diploids nicely, but we haven't thought nearly as much about how to indicate to human users that something is done in a diploid. (Let's keep that separate from this ticket if possible, though.)

[Kim Rutherford]

A wild type allele can only have endogenous expression if there is another copy
of the same gene in the genotype

I guess that should say?: A wild type allele can only have endogenous expression if there is a another wild type allele in the genotype that has non-endogenous expression.

I'm implementing that now.

What should happen if a genotype has:
wild type cdc2 (Overexpressed)
wild type cdc2 (Endogenous)

and then I delete the Overexpressed allele?

Although I might not worry about that for now as we can check for small screw ups like that on loading.

[Kim Rutherford]

Endogenous expression is now an option for the second (and subsequent) wild type allele of a gene.
https://github.com/pombase/canto/commit/17684265012da66d8b04fc49eab8d5376b5b8952

Currently it's possible to create a wild type allele with no expression (ie. not even Endogenous). Should that be disallowed?

[Valerie Wood]

I don't think it should be allowed...

[Kim Rutherford]

OK, wild type allele must now have an expression.

[Valerie Wood]

Delete it from the session, or delete it from the database?

[Kim Rutherford]

Delete it from the session, or delete it from the database?

I just meant deleting from the list of alleles on screen while building up a genotype on the genotype creation page. If there was wild type endogenous and wild type overexpressed allele of a gene in the list, I guess you shouldn't be able to delete the overexpressed allele because the genotype then becomes invalid.

[Valerie Wood]

I'm confused, did I post this in the wrong ticket?

[Kim Rutherford]

I don't think it was the wrong ticket. I said "and then I delete the Overexpressed allele?" and you asked where it was going to be deleted from.

[Valerie Wood]

If I understood correctly, this would be the corrrect behavior

I guess you shouldn't be able to delete the overexpressed allele because the genotype then becomes invalid.

v

[Kim Rutherford]

OK, closing this and I've made a ticket about better checking for consistency:

https://sourceforge.net/p/pombase/curation-tool/800/