report any WT phenotypes with no "knockdown" or "overexpression" in logs

[ValWood]

https://github.com/pombase/curation/issues/851

[ValWood]

Add 'discuss' back if you need to discuss.

[kimrutherford]

"knockdown" or "overexpression"

We have 613 genotypes with an allele with the expression recorded as "Not assayed or wild type". And 6 as "Ectopic".

How do they fit in?

---

Note to self, query for allele and expression where the expression level isn't "Overexpression" OR "Knockdown". A query like this could be added as a Chado Check in load-pombase-chado.yaml:

WITH allele_and_expression as (
SELECT allele.uniquename,
(SELECT expression_prop.value FROM feature_relationshipprop expression_prop
   JOIN cvterm expression_prop_type ON expression_prop.type_id = expression_prop_type.cvterm_id
  WHERE expression_prop_type.name = 'expression'
    AND expression_prop.feature_relationship_id = rel.feature_relationship_id) as expression
FROM feature allele
JOIN featureprop allele_type_prop ON allele_type_prop.feature_id = allele.feature_id
JOIN cvterm allele_type_cvterm ON allele_type_cvterm.cvterm_id = allele_type_prop.type_id
JOIN feature_relationship rel ON rel.subject_id = allele.feature_id
JOIN feature genotype ON genotype.feature_id = rel.object_id
JOIN feature_cvterm fc ON genotype.feature_id = fc.feature_id
JOIN cvterm genotype_cvterm ON genotype_cvterm.cvterm_id = genotype.type_id
WHERE allele.type_id IN (SELECT cvterm_id FROM cvterm WHERE name = 'allele')
  AND allele_type_cvterm.name = 'allele_type'
  AND allele_type_prop.value = 'wild_type'
  AND genotype_cvterm.name = 'genotype')
SELECT * FROM allele_and_expression
WHERE expression <> 'Overexpression' AND expression <> 'Knockdown';

[ValWood]

We have 613 genotypes with an allele with the expression recorded as "Not assayed or wild type". And 6 as "Ectopic".

With WT alleles?

[kimrutherford]

With WT alleles?

Yep, I queried for WT alleles only. Sorry I wasn't clear.

[ValWood]

OK, it's kind of weird that we have so many because we don't curate WT unless the expression is changed? Can you give us the list?

[kimrutherford]

OK, it's kind of weird that we have so many because we don't curate WT unless the expression is changed?

Most (maybe all, I haven't checked) are from multi-allele or multi-locus genotypes:

• https://www.pombase.org/genotype/tor2%2B%28wild_type%29-expression-not_assayed_or_wild_type_tor2delta
• https://www.pombase.org/genotype/tor2%2B%28wild_type%29-expression-not_assayed_or_wild_type__tor2-HTHdelta-710-734-partial_amino_acid_deletion-expression-not_assayed_or_wild_type

[ValWood]

OK I think most of these are heterozygous diploids where one WT copy is retained. In all of these cases we can assume WT expression for the WT alleles. If we take these away how many are left?

[kimrutherford]

If we take these away how many are left?

After removing the diploids there are 80 WT alleles that are "Not assayed or wild type". From a quick look most of them look like they are part of multi locus genotypes:

• https://www.pombase.org/genotype/slp1%2B%28wild_type%29-expression-not_assayed_or_wild_type__slp1-mr63-A131P,F132T-amino_acid_mutation-expression-not_assayed_or_wild_type
• https://www.pombase.org/genotype/rtf1%2B%28wild_type%29-expression-not_assayed_or_wild_type__rtf1-R346*-R346*-partial_amino_acid_deletion-expression-not_assayed_or_wild_type

[kimrutherford]

And there are 11 alleles that are "Not assayed or wild type" in a single allele haploid genotype. These links will work today only. I'm happy to update the table later if needed.

name	uniquename
SPAC1B9.03c+	https://www.pombase.org/allele/SPAC1B9.03c:allele-2
SPBC609.01+	https://www.pombase.org/allele/SPBC609.01:allele-2
brf1+	https://www.pombase.org/allele/SPBC13E7.10c:allele-2
cdc18+	https://www.pombase.org/allele/SPBC14C8.07c:allele-17
cnd1+	https://www.pombase.org/allele/SPBC776.13:allele-14
hht1+	https://www.pombase.org/allele/SPAC1834.04:allele-2
mug65+	https://www.pombase.org/allele/SPAC1296.04:allele-2
peg1+	https://www.pombase.org/allele/SPAC3G9.12:allele-2
pmo25+	https://www.pombase.org/allele/SPAC1834.06c:allele-4
pob1+	https://www.pombase.org/allele/SPBC1289.04c:allele-3
teb1+	https://www.pombase.org/allele/SPAC13G7.10:allele-2

---

Note to self:

WITH allele_and_expression AS
  (SELECT allele.name, allele.uniquename,
     (SELECT expression_prop.value
      FROM feature_relationshipprop expression_prop
      JOIN cvterm expression_prop_type ON expression_prop.type_id = expression_prop_type.cvterm_id
      WHERE expression_prop_type.name = 'expression'
        AND expression_prop.feature_relationship_id = rel.feature_relationship_id) AS expression
   FROM feature allele
   JOIN featureprop allele_type_prop ON allele_type_prop.feature_id = allele.feature_id
   JOIN cvterm allele_type_cvterm ON allele_type_cvterm.cvterm_id = allele_type_prop.type_id
   JOIN feature_relationship rel ON rel.subject_id = allele.feature_id
   JOIN feature genotype ON genotype.feature_id = rel.object_id
   JOIN feature_cvterm fc ON genotype.feature_id = fc.feature_id
   JOIN cvterm genotype_cvterm ON genotype_cvterm.cvterm_id = genotype.type_id
   WHERE allele.type_id IN (SELECT cvterm_id FROM cvterm WHERE name = 'allele')
     AND allele_type_cvterm.name = 'allele_type'
     AND allele_type_prop.value = 'wild_type'
     AND genotype_cvterm.name = 'genotype'
     AND rel.feature_relationship_id NOT IN
       (SELECT feature_relationship_id
        FROM feature_relationshipprop
        WHERE value IN
            (SELECT p.value
             FROM feature_relationshipprop p
             JOIN feature_relationship rel ON rel.feature_relationship_id = p.feature_relationship_id
             WHERE p.type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'genotype_locus')
             GROUP BY p.value
             HAVING count(rel.feature_relationship_id) > 1))
     AND genotype.feature_id NOT IN
       (SELECT object_id
        FROM feature_relationship
        WHERE object_id IN
            (SELECT feature_id
             FROM feature
             WHERE type_id IN
                 (SELECT cvterm_id
                  FROM cvterm
                  WHERE name = 'genotype'))
        GROUP BY object_id
        HAVING count(feature_relationship_id) > 1) )
SELECT DISTINCT name, uniquename
FROM allele_and_expression
WHERE expression <> 'Overexpression'
  AND expression <> 'Knockdown'
  AND expression <> 'Ectopic';

[PCarme]

And there are 11 alleles that are "Not assayed or wild type" in a single allele haploid genotype. These links will work today only. I'm happy to update the table later if needed.

name uniquename SPAC1B9.03c+ https://www.pombase.org/allele/SPAC1B9.03c:allele-2 SPBC609.01+ https://www.pombase.org/allele/SPBC609.01:allele-2 brf1+ https://www.pombase.org/allele/SPBC13E7.10c:allele-2 cdc18+ https://www.pombase.org/allele/SPBC14C8.07c:allele-17 cnd1+ https://www.pombase.org/allele/SPBC776.13:allele-14 hht1+ https://www.pombase.org/allele/SPAC1834.04:allele-2 mug65+ https://www.pombase.org/allele/SPAC1296.04:allele-2 peg1+ https://www.pombase.org/allele/SPAC3G9.12:allele-2 pmo25+ https://www.pombase.org/allele/SPAC1834.06c:allele-4 pob1+ https://www.pombase.org/allele/SPBC1289.04c:allele-3 teb1+ https://www.pombase.org/allele/SPAC13G7.10:allele-2

Most of these come from the same publication https://www.pombase.org/reference/PMID:29735745 And a couple are used in rescue experiments, in diploid genotypes with a deletion of the same gene, like https://www.pombase.org/genotype/brf1%2B%28wild_type%29-expression-not_assayed_or_wild_type_brf1delta

[PCarme]

The ones that come from this paper https://www.pombase.org/reference/PMID:29735745 are actually promoter swapped WT alleles for which the expression level is either the same as with the endogenous promoter or not assayed.

[ValWood]

Maybe we can just dleete the ones that are not diploids. Do they capture anything useful?

[PCarme]

The ones that come from this paper https://www.pombase.org/reference/PMID:29735745 are actually promoter swapped WT alleles for which the expression level is either the same as with the endogenous promoter or not assayed.

Those from this paper (session f5cfe860f60d0109) don't seem too useful, they are all annotated to normal phenotypes so they don't seem to capture anything special. One of them could actually be turned into WT expression level in the allele description.

I will have a look at the annotations to the other haploid ones.

[PCarme]

Looks like these alleles have no useful annotations. https://www.pombase.org/genotype/SPAC1B9.03c%2B%28wild_type%29-expression-not_assayed_or_wild_type https://www.pombase.org/genotype/SPBC609.01%2B%28wild_type%29-expression-not_assayed_or_wild_type https://www.pombase.org/genotype/brf1%2B%28wild_type%29-expression-not_assayed_or_wild_type https://www.pombase.org/genotype/cnd1%2B%28wild_type%29-expression-not_assayed_or_wild_type https://www.pombase.org/genotype/peg1%2B%28wild_type%29-expression-not_assayed_or_wild_type https://www.pombase.org/genotype/pmo25%2B%28wild_type%29-expression-not_assayed_or_wild_type https://www.pombase.org/genotype/pob1%2B%28wild_type%29-expression-not_assayed_or_wild_type https://www.pombase.org/genotype/teb1%2B%28wild_type%29-expression-not_assayed_or_wild_type

I have to look at these papers/sessions for the other haploid alleles. https://www.pombase.org/reference/PMID:9303312 https://www.pombase.org/reference/PMID:32152323 https://www.pombase.org/reference/PMID:36095128

[PCarme]

For this allele https://www.pombase.org/genotype/cdc18%2B%28wild_type%29-expression-not_assayed_or_wild_type, I fixed some annotations relating to the level of WT RNA of cdc18. The last annotation to this genotype describes an effect of HU treatment on MBF complex assembly in WT cells.

[ValWood]

The last annotation to this genotype describes an effect of HU treatment on MBF complex assembly in WT cells.

Yeah that can go...

[PCarme]

This one https://www.pombase.org/genotype/hht1%2B%28wild_type%29-expression-not_assayed_or_wild_type captures a phenotype of having hht1 expressed by the hht2 promoter, with the effect on expression not assayed

[PCarme]

And this one https://www.pombase.org/genotype/mug65%2B%28wild_type%29-expression-not_assayed_or_wild_type captures the retention of an intron of mug65 in WT cells at high temperature

[ValWood]

And this one https://www.pombase.org/genotype/mug65%2B%28wild_type%29-expression-not_assayed_or_wild_type captures the retention of an intron of mug65 in WT cells at high temperature

deleted!

[kimrutherford]

Updated table from latest Chado, with working links:

name	uniquename
SPAC1B9.03c+	https://www.pombase.org/allele/SPAC1B9.03c:allele-2
SPBC609.01+	https://www.pombase.org/allele/SPBC609.01:allele-2
brf1+	https://www.pombase.org/allele/SPBC13E7.10c:allele-2
cnd1+	https://www.pombase.org/allele/SPBC776.13:allele-3
hht1+	https://www.pombase.org/allele/SPAC1834.04:allele-8
peg1+	https://www.pombase.org/allele/SPAC3G9.12:allele-2
pmo25+	https://www.pombase.org/allele/SPAC1834.06c:allele-3
pob1+	https://www.pombase.org/allele/SPBC1289.04c:allele-2
teb1+	https://www.pombase.org/allele/SPAC13G7.10:allele-2

[PCarme]

Updated table from latest Chado, with working links:

name uniquename SPAC1B9.03c+ https://www.pombase.org/allele/SPAC1B9.03c:allele-2 SPBC609.01+ https://www.pombase.org/allele/SPBC609.01:allele-2 brf1+ https://www.pombase.org/allele/SPBC13E7.10c:allele-2 cnd1+ https://www.pombase.org/allele/SPBC776.13:allele-3 hht1+ https://www.pombase.org/allele/SPAC1834.04:allele-8 peg1+ https://www.pombase.org/allele/SPAC3G9.12:allele-2 pmo25+ https://www.pombase.org/allele/SPAC1834.06c:allele-3 pob1+ https://www.pombase.org/allele/SPBC1289.04c:allele-2 teb1+ https://www.pombase.org/allele/SPAC13G7.10:allele-2

I think the hht1 allele is the only one of these that captures a real phenotype. The ones from this publication https://www.pombase.org/reference/PMID:29735745 all seem pretty useless to me.

[kimrutherford]

Updated table from latest Chado, with working links:

I've add a new log file for this. Look for a file ending in .chado_checks.single_wt_allele_with_wild_type_expression:

https://curation.pombase.org/dumps/builds/pombase-build-2024-07-25/logs/log.2024-07-24-18-51-33.chado_checks.single_wt_allele_with_wild_type_expression

[ValWood]

OK, remove those from https://www.pombase.org/reference/PMID:29735745

does hht1 have different expression?

[PCarme]

OK, remove those from https://www.pombase.org/reference/PMID:29735745

That's done now. I only left the cnd1 promoter swap allele in the session as I just realised that it is used in a genetic interaction with another mutation.

does hht1 have different expression?

The promoter swapping affects the dynamics of Hht1 expression during germination.