extracting dominant alleles

[ValWood]

SET5 All dominant heterozygous diploids
Extract all heterozygous diploid alleles (where only one is WT) and "abnormal phenotype"

Rationale, any abnormal phenotype in the heterozygote will be dominant, even if present in the homozygote

Allele name, allele description, genename, sys ID, expression level, conditions, fypo_ID, fypo_term_name PMID

Generate nightly and include in the monthly release

Use the diploid file format

[kimrutherford]

Does it make a difference which conditions are annotated for the phenotype?

[ValWood]

I don't think so @PCarme ?

[kimrutherford]

I forgot that I started implementing this a while ago so we have this nightly file already:
https://curation.pombase.org/dumps/latest_build/misc/dominant_diploid_annotations.tsv

I this it's correct but it doesn't include the phenotypes that are annotated to child terms of "abnormal phenotype". I'm working on that now.

[kimrutherford]

I forgot that I started implementing this a while ago so we have this nightly file already:
https://curation.pombase.org/dumps/latest_build/misc/dominant_diploid_annotations.tsv

In the current code if the non-WT allele has NULL expression, the diploid isn't included in the output. Is that correct?

[PCarme]

Does it make a difference which conditions are annotated for the phenotype?

Probably not. Even if the phenotype is only visible in certain conditions, as long as it is observed in a heterozygous diploid, it is still a dominant allele.

[PCarme]

I forgot that I started implementing this a while ago so we have this nightly file already:
https://curation.pombase.org/dumps/latest_build/misc/dominant_diploid_annotations.tsv

In the current code if the non-WT allele has NULL expression, the diploid isn't included in the output. Is that correct?

That would be a case of haploinsufficiency, which is a type of dominant allele, so I think it should be in the dominant allele file.
@ValWood Do you agree ?

[ValWood]

Do you agree ?

Yes, I missed this question

[kimrutherford]

https://curation.pombase.org/dumps/latest_build/misc/dominant_diploid_annotations.tsv

I this it's correct but it doesn't include the phenotypes that are annotated to child terms of "abnormal phenotype".

I had the code wrong so please ignore that file. It includes normal phenotypes.

[kimrutherford]

Thanks.

Here's what the file looks like when the null expression alleles and the child terms of "abnormal phenotype" are included. There's only 70?:

https://curation.pombase.org/kmr44/dominant_diploid_annotations-example.tsv

[ValWood]

That seems low. Did we have more in previus versions of the file?