Quantitive copy number for expression

[ValWood]

Found in my pending file:

Dear xxx,

Thanks for getting in touch. Usually we can reopen the session for you to add curation. Unfortunately we cannot capture quantitive copy number in Canto yet (only qualitative). We will add it very soon because we needed it for 2 other community sessions yesterday. We had been meaning to do this but it fell off our radar.

You can supply me the genes and RNA/protein levels as a 2 column list and I can make file to import in this format

https://www.pombase.org/documentation/quantitative-gene-expression-data-bulk-upload-format

We hope to make this curation type available in Canto very soon.

[ValWood]

author: We measured the total cell concentration in EMM at room temperature in wild-type cells:

Pil1p-mEGFP: 619,000 ± 60,300 molecules/cell, or 38.2 ± 3.7 μM global concentration (mean ± SD across six images, 150 cells).

We can only report the total cell copy number, not the local copy number/density in the subcellular structure (eisosomes), or the cytoplasmic concentration, correct?

Also, we cannot add other quantitative information like rate constants, correct?

[ValWood]

Correct. At present we cannot capture either of these. Although we did discuss yesterday capturing local concentrations. I will open a ticket about this and if we do it we can go back to this paper and use it as an test case.

I can add the rate constant as a comment which will appear on the gene page and the publication page even though we have not a formal curation "type" for this.

[ValWood]

So I think we decided in this case, we could not capture local concentrations, but, we would still want to be able to capture numbers in canto. This isn't at all urgent because if necessary we can do in an import file,