"Not assayed", "expression present, level unknown" or "expression level unknown"

[Hsinyugithub]

Do we need "Not assayed", "expression present, level unknown" or "expression level unknown" as an option for expression level?

Example1:
Ethyl methanesulfonate(EMS) mutagenesis mutants [PMID:38265007].

Example 2: [PMID:21623954]
The 5-29H mutant has a T-DNA insertion within a predicted Alg2-like mannosyltransferase gene.

Example 3: [PMID: 17073308]
Disruption

[jseager7]

I can't really comment on the above examples because I don't understand the biology. @martin2urban please can you give your opinions on the above examples?

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In terms of the logic of this: for cases when the expression is present but the level is definitely unknown, then 'Level unknown' seems like a sensible label. However, in PHI-Canto, it sounds like the 'Expression' of an allele is the level of expression, not the presence or absence of expression.

Here's what the Canto help page says:

"Expression: you will be prompted to define the expression level relative to wild-type (deletion mutants are automatically set to null). Note that ‘expression’ refers to the amount of gene product present in the assayed cells. If the product level was not measured (e.g. by Western blot for a protein), choose ‘Not assayed’, even if a construct such as an inducible promoter was used to try to alter expression."

That means 'Not assayed' really means 'Expression level not assayed'. This would make 'Level unknown' redundant (if we assume that the only way that the level can be unknown is if it hasn't been assayed).

So maybe the problem is we have no way of indicating when the publication has nothing at all about the expression, not even presence or absence? Please let me know If I've misunderstood.

[Hsinyugithub]

I agree that 'Expression level not assayed' is much better than "Not assayed". I think this is more clear for the users.

[Hsinyugithub]

We have discussed this in the lab meeting. Kim suggested that we could use "‘Expression present, level not assayed’" instead. https://docs.google.com/document/d/1N-oah0pbHuNuZtoke1SBEbnLZyl5pmfSit-nxsC8G04/edit?tab=t.0