UBERON:0000125
From FANTOM5_SSTAR
| Name: | neural nucleus | |
|---|---|---|
| Namespace: | FANTOM | |
| Definition: | "Anatomical structure consisting of a discrete aggregate of neuronal soma[GO]." [GO:0048857, GO_REF:0000021, Wikipedia:Nucleus_(neuroanatomy)] | |
| Xrefs: |
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| Synonyms: |
"neuraxis nucleus" EXACT [FMA:83686] "nucleus" BROAD [] "nucleus of neuraxis" RELATED [] | |
| Comments: | do not include NIF_Subcellular:sao1702920020 Nucleus. Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in "subcortical" because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in "relatively compact" and "distiguishable by histology" because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate. |
Ontology association<br>Each term has an is_a parent in the Uberon Ontology, which has a linkage to an another entity and FANTOM5 samples.Libraries were grouped into mutually exclusive facets according to the FANTOM5 sample ontology mapping to UBERON ontologies.<br><br>link to ontology dataset<br>data
Parents
| is_a: | UBERON:0011215(central nervous system cell part cluster) |
|---|---|
| part_of: | UBERON:0001017(central nervous system) |
Children
| is a: | UBERON:0002308 (nucleus of brain) |
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Ontology Tree: Loaded from BioPortal
Ontorolgy tree(Small window open)
FF samples<br>It includes FANTOM5 samples that overlay the Uberon ontology
Human (Homo sapiens)
- 10037-101F1 (nucleus accumbens, adult, pool1)
- 10152-102I8 (putamen, adult, donor10252)
- 10158-103A5 (substantia nigra, adult, donor10252)
- 10161-103A8 (globus pallidus, adult, donor10252)
- 10164-103B2 (caudate nucleus, adult, donor10252)
- 10165-103B3 (locus coeruleus, adult, donor10252)
- 10175-103C4 (globus pallidus - adult, donor10196)
- 10176-103C5 (putamen, adult, donor10196)
- 10177-103C6 (caudate nucleus - adult, donor10196)
- 10178-103C7 (substantia nigra - adult, donor10196)
... further results Mouse (Mus musculus)
- 10037-101F1 (nucleus accumbens, adult, pool1)
- 10152-102I8 (putamen, adult, donor10252)
- 10158-103A5 (substantia nigra, adult, donor10252)
- 10161-103A8 (globus pallidus, adult, donor10252)
- 10164-103B2 (caudate nucleus, adult, donor10252)
- 10165-103B3 (locus coeruleus, adult, donor10252)
- 10175-103C4 (globus pallidus - adult, donor10196)
- 10176-103C5 (putamen, adult, donor10196)
- 10177-103C6 (caudate nucleus - adult, donor10196)
- 10178-103C7 (substantia nigra - adult, donor10196)
Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with UBERON:0000125 (neural nucleus), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data
