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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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chromosome number maintenence #11062

Closed gocentral closed 9 years ago

gocentral commented 10 years ago

defined as The maintenance of the standard number of chromosomes in a cell.

sounds like a phenotype, not a process?

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/10877

gocentral commented 10 years ago

...has no annotations, val

Original comment by: ValWood

gocentral commented 10 years ago

Original comment by: dosumis

gocentral commented 10 years ago

'increased chromosome number and 'decreased chromosome number' are phenotypes. 'maintenance of chromosome number' is not. Whether this term should exist hinges on whether we can describe an endogenous process that functions to keep chromosomal number stable.

I can certainly see how the term might attract annotation to phenotypes that only very indirectly affect chromosome number. There are no annotations right now, so we could obsolete without too much hassle.

Having some idea about the intention behind this term would help in judging whether there is some endogenous process that fits the bill. In the absence of a reference on the term or any annotations, the only clue that I can see is in the synonyms:

synonym: "diploidization" RELATED [GOC:tb] synonym: "haploidization" RELATED [GOC:tb]

'regulation of ploidy' could, I think, be seen as an endogenous process. e.g. endoreduplication is regulated by cell type in insects. So this seems like a more useful term to have.

Perhaps obsolete the existing term and add 'regulation of ploidy' with diploidization, haploidization and endoreduplication as children ? May be more hassle than its worth though as some major changes to the graph are likely to be necessary to incorporate

Original comment by: dosumis

gocentral commented 10 years ago

I was thinking about this last night. I think we have such a process:

GO:0032876 negative regulation of DNA endoreduplication

is the process which maintains ploidy?

Original comment by: ValWood

gocentral commented 10 years ago

DNA endoreduplication

is defined

Regulated re-replication of DNA within a single cell cycle, resulting in an increased cell ploidy. An example of this process occurs in the synthesis of Drosophila salivary gland cell polytene chromosomes.

Original comment by: ValWood

gocentral commented 10 years ago

David,

Isn't 'maintenance of chromosome number' effectively a synonym of chromosome segregation ? The cell aims to do this such that both cells get the same number of chromosomes...

what do you think ?

Original comment by: pgaudet

gocentral commented 10 years ago

I though this at first, but this would be an anuploidy-type phenotype for chromosome mis-segregation process (which would always be a phenotype). I only realised later it was for 'maintenance of ploidy' more generally. So there are instances where this is a process, but I now think it is more accurately described as negative regulation of re-replication.

Original comment by: ValWood

gocentral commented 10 years ago

Original comment by: dosumis

gocentral commented 10 years ago

This term will be obsoleted. In the paper that motivated the addition of this term (http://www.ncbi.nlm.nih.gov/pubmed/15138769) it seems that the phenotype - increase in chromosome number is the result of nuclear fusion - so if there is an endogenous process it is to do with the prevention of nuclear fusion. Also, this phenotype is relatively rare under normal circumstances, so can not be considered cannonical.

Original comment by: dosumis

gocentral commented 10 years ago

Original comment by: dosumis