Fixes #2651 NTR diffuse bipolar 5 cell #2664
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Fixes #2651 NTR diffuse bipolar 5 cell
aleixpuigb
added
new term request
HCA/DCP
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MYO16 marker can be found in the article supplementary figure: |
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I think we need to have a discussion of what we mean by a marker gene. In the figure above, MYO16 is also expressed at lower levels in a few other bipolar cells. But in the image below, it is also highly expressed in several amacrine cell types in the Li et al. dataset. So what would we assert in this case? |
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Thank you @scheuerm.
The reason that I used this gene was because the Single Cell Atlas of the Human Retina are using MYO16 as a canonical marker for this cell type. They also provide a gene set for DB5 (CDH18, COL19A1, DOK5, HDAC2-AS2, HS3ST5) that is more enriched, but it is also enriched at lower levels in other cell types: However, one of the markers, COL19A1, seems to be highly expressed but misses some cells (6700/52000, 13%): Seeing this, do you think a single gene (COL19A1) would be a good marker, or having the set of markers would be more robust? A set of markers for all retinal cells identified by NS-Forest would really be great! |
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@aleixpuigb Let's discuss. |
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -simple file):Ontology comparisonLeft
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Ontology importsOntology annotationsdiffuse bipolar 5 cell
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsdiffuse bipolar 5 cell
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@aleixpuigb , COL19A1 is one of the combo markers selected by NS-Forest. Here are the data for the combo:
The F-beta score of 0.91 is very high, but as with most markers in these single cell datasets, false negative calls result in lower recall. But COL19A1 would be much better than MYO16. |
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This is great, thank you @scheuerm! |
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27833534") rdfs:comment obo:CL_4033085 "A diffuse bipolar 5 cell typically contacts 7–8 cone photoreceptors. The number and thickness of its dendritic processes are intermediate between those of a diffuse bipolar 6 cell (less dense and thinner) and a diffuse bipolar 4 cell (denser and thicker).") | ||
| AnnotationAssertion(rdfs:label obo:CL_4033085 "diffuse bipolar 5 cell") | ||
| SubClassOf(obo:CL_4033085 obo:CL_0000749) | ||
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PMID: 29114208
This reference might have some extra synonyms such as Type 5, T5 but unsure if you want to associate to diffuse bipolar cells, these are referred to as bipolar cells.
also it subdivide them further into type 5 inner (5i), outer (5o) and thick (5t) types.
just a suggestion.
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Thank you for the suggestion. These synonyms are for the mouse type 5 bipolar cell, and the subclasses are orthologs of DB5, DB4a and DB4b. However, I will look into adding them in a separate ticket.
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After discussing with the other CL ontology editors, we agreed that having the NS-Forest markers would be ideal, but we need a published reference to use them. Once the data for all retinal cells is available, we can include them all. Temporally, to have the term available for annotation, we will have in the definition MYO16 as a marker to distinguish ONLY with other bipolar cells. Thank you for all your feedback @scheuerm, this discussion was very helpful not only for this term, but for the terms to come. |
MYO16 marker is not good to compare with other retinal cells, and it is also lowly expressed in other bipolar cells, so a further clarification was needed.
Fixes #2651 NTR diffuse bipolar 5 cell