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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Make sex-chromosome dosage compensation do not annotate #26961

Open cmungall opened 9 months ago

cmungall commented 9 months ago

There is no reason to annotate to this directly. You always know the mechanism based on the species

There are 25 direct experimental annotations that could be auto pushed down https://amigo.geneontology.org/amigo/term/GO:0007549

Oddly there are a lot of IBAs to brca1 even though the IBD source uses a mechanism specific term. IMO the source Brca1 annotation seems not quite right

pgaudet commented 9 months ago

autopush down to which term?

ValWood commented 2 weeks ago

waiting for response from @cmungall

cmungall commented 2 weeks ago

Dmel: GO:0009047 ! dosage compensation by hyperactivation of X chromosome Mammals: GO:0009048 ! dosage compensation by inactivation of X chromosome C elegans: GO:0042464 ! dosage compensation by hypoactivation of X chromosome

It may be possible to sometimes further pushdown the mammalian annotations further to random vs imprinted, this is quite interesting, but outside the scope of this simple ticket.

Separate from this, do we believe the annotations here? Is BRCA1 really involved or is this downstream of its normal role? https://amigo.geneontology.org/amigo/reference/PMID:12419249

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deustp01 commented 2 weeks ago

From the PubMed abstract

BRCA1, a breast and ovarian tumor suppressor, colocalizes with markers of the inactive X chromosome (Xi) on Xi in female somatic cells and associates with XIST RNA, as detected by chromatin immunoprecipitation. Breast and ovarian carcinoma cells lacking BRCA1 show evidence of defects in Xi chromatin structure. Reconstitution of BRCA1-deficient cells with wt BRCA1 led to the appearance of focal XIST RNA staining without altering XIST abundance. Inhibiting BRCA1 synthesis in a suitable reporter line led to increased expression of an otherwise silenced Xi-located GFP transgene. These observations suggest that loss of BRCA1 in female cells may lead to Xi perturbation and destabilization of its silenced state.

So the assertion is that BRCA1 gene product, by joining a complex, changes the behavior of that complex so that dosage commpensation is perturbed.