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New Term Request TAC3-positive medium spiny neurons #2304

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merged 9 commits into from
Mar 25, 2024
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@AvolaAmg AvolaAmg commented Mar 4, 2024

Fixes #2301

New Term Request TAC3-positive medium spiny neurons
@AvolaAmg AvolaAmg self-assigned this Mar 4, 2024
@AvolaAmg AvolaAmg changed the title Fixes #2301 New Term Request TAC3-positive medium spiny neurons Mar 4, 2024
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AvolaAmg commented Mar 4, 2024

#gogoeditdiff

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github-actions bot commented Mar 4, 2024

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-03-04/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-03-04/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

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CL_4042001 http://purl.obolibrary.org/obo/CL_4042001

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github-actions bot commented Mar 4, 2024

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

CL_4042001 http://purl.obolibrary.org/obo/CL_4042001

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dosumis commented Mar 4, 2024

Is there some consensus on a short name for these neurons yet?

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AvolaAmg commented Mar 4, 2024

No there is not. Should I check with people from the BRAIN data standards slack?

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Thank you for this new term. Please, consider the suggested changes.

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What does enriched expression mean? Are these cells also found in other brain regions? Are these genes also expressed in equivalent cell types in other species?

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What does enriched expression mean? Are these cells also found in other brain regions? Are these genes also expressed in equivalent cell types in other species?

@scheuerm

Thanks for you comment

In PMID:34727523

Differential gene analysis of the D1Sh TAC3 archetype revealed selectively enriched genes in this archetype, including MPPED1, HPCAL1, and MEIS3. This result demonstrates within-subtype variations with potentially functional roles.

I hope this helps to clarify. With enriched expression, it is intended an increased expression of these specific genes in the D1Sh TAC3 archetype (cell type identified through archetype analysis) after performing Differential gene expression analysis. In particular the D1Sh TAC3 archetype was found between the two set of samples they acquired in this dataset. Afterwards, they performed a Dirichlet Simplex Nest (DSN) analysis to identify the distribution of gene expression cross cell archetypes. The molecular markers MPPED1, HPCAL1, MEIS3 were found by performing gene’s Pearson correlation with each archetype of interest.

The TAC3+ Medium spiny neurons are described in PMID:34727523. So far it seems to be the only paper that describes this cell type, therefore there is no additional information in the literature that the molecular signature of these neurons is found 1) in other brain regions and 2) in other species.

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Please, see inline comments.

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@AvolaAmg AvolaAmg merged commit dd07342 into master Mar 25, 2024
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@AvolaAmg AvolaAmg deleted the Fixes-#2301 branch March 25, 2024 16:44
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[NTR] TAC3-positive medium spiny neurons
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