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{{UBERON
{{UBERON
|id=UBERON:0000125
|alt_id=
|name=neural nucleus
|anatomical_img_id=FMA:83686
|namespace=
|def="Anatomical structure consisting of a discrete aggregate of neuronal soma[GO]." [GO:0048857, GO_REF:0000021, Wikipedia:Nucleus_(neuroanatomy)]
|xref=FMA:83686
|is_a=UBERON:0000064;;UBERON:0000073
|synonym="neuraxis nucleus" EXACT [FMA:83686];;"nucleus" BROAD [];;"nucleus of neuraxis" RELATED []
|comment=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.
|comment=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.
|alt_id=
|disjoint_from=
|union_of=
|created_by=
|created_by=
|obo_creation_date=
|def="Anatomical structure consisting of a discrete aggregate of neuronal soma[GO]." [GO:0048857, GO_REF:0000021, Wikipedia:Nucleus_(neuroanatomy)]
|subset=
|adjacent_to=
|derives_from=
|derives_from=
|develops_from=
|develops_from=
|disjoint_from=
|has_quality=
|has_quality=
|id=UBERON:0000125
|is_a=UBERON:0011215
|is_obsolete=
|located_in=
|located_in=
|part_of=UBERON:0001016
|name=neural nucleus
|namespace=FANTOM
|obo_creation_date=
|part_of=UBERON:0001017
|preceded_by=
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|subset=
|synonym="neuraxis nucleus" EXACT [FMA:83686];;"nucleus" BROAD [];;"nucleus of neuraxis" RELATED []
|union_of=
|xref=FMA:83686
}}
}}

Latest revision as of 17:06, 12 September 2014

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:
links:
FMA:83686
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)

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)

... further results Mouse (Mus musculus)

... further results


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

P-valueFFCPShort description
6.51e-112FFCP PHASE2:Hg19::chr2:7112752..7112770,+#_02a34646a603f9b7b12a630daf3edbc2p@chr2:7112752..7112770, +
6.51e-112FFCP PHASE1:Hg19::chr2:7112752..7112770,+#_02a34646a603f9b7b12a630daf3edbc2p@chr2:7112752..7112770, +
7.88e-112FFCP PHASE2:Hg19::chr22:27727810..27727817,+#_df047eec61dba902e91f9f705026b181p3@ENST00000413244
7.88e-112FFCP PHASE1:Hg19::chr22:27727810..27727817,+#_df047eec61dba902e91f9f705026b181p3@ENST00000413244
4.6e-109FFCP PHASE2:Hg19::chr15:35546024..35546035,-#_d23b414bfac5ec82116a13a1b9b60986p@chr15:35546024..35546035, -
4.6e-109FFCP PHASE2:Hg19::chr2:3853961..3853984,+#_d23b414bfac5ec82116a13a1b9b60986p@chr2:3853961..3853984, +
4.6e-109FFCP PHASE1:Hg19::chr17:19390211..19390223,+#_d23b414bfac5ec82116a13a1b9b60986p@chr17:19390211..19390223, +
4.6e-109FFCP PHASE2:Hg19::chr17:19390211..19390223,+#_d23b414bfac5ec82116a13a1b9b60986p@chr17:19390211..19390223, +
4.6e-109FFCP PHASE1:Hg19::chr15:35546024..35546035,-#_d23b414bfac5ec82116a13a1b9b60986p@chr15:35546024..35546035, -
4.6e-109FFCP PHASE1:Hg19::chr2:3853961..3853984,+#_d23b414bfac5ec82116a13a1b9b60986p@chr2:3853961..3853984, +
6.41e-107FFCP PHASE2:Hg19::chr2:220197419..220197439,-#_6fc5ed6127a76e5320dd56bfd607ed6bp2@RESP18
6.41e-107FFCP PHASE1:Hg19::chr2:220197419..220197439,-#_6fc5ed6127a76e5320dd56bfd607ed6bp2@RESP18
3.33e-98FFCP PHASE2:Hg19::chr11:18765839..18765846,-#_586cf29d8b306b3acf7697f8f8f15980p10@PTPN5
3.33e-98FFCP PHASE1:Hg19::chr11:18765839..18765846,-#_586cf29d8b306b3acf7697f8f8f15980p10@PTPN5
4.08e-91FFCP PHASE2:Hg19::chr11:26497871..26497889,+#_8a0831d3aefef1a8bcce8eba3978a925p@chr11:26497871..26497889, +
4.08e-91FFCP PHASE2:Hg19::chr10:97261901..97261919,-#_8a0831d3aefef1a8bcce8eba3978a925p@chr10:97261901..97261919, -
4.08e-91FFCP PHASE1:Hg19::chr11:26497871..26497889,+#_8a0831d3aefef1a8bcce8eba3978a925p@chr11:26497871..26497889, +
4.08e-91FFCP PHASE1:Hg19::chr10:97261901..97261919,-#_8a0831d3aefef1a8bcce8eba3978a925p@chr10:97261901..97261919, -
4.91e-91FFCP PHASE2:Hg19::chr22:24828830..24828842,+#_d4a2c9ba061b51df18720df323a6968ap14@ADORA2A
4.91e-91FFCP PHASE2:Hg19::chr1:242372439..242372456,+#_d4a2c9ba061b51df18720df323a6968ap1@ENST00000421878
4.91e-91FFCP PHASE2:Hg19::chr11:26495467..26495474,+#_d4a2c9ba061b51df18720df323a6968ap8@ANO3
4.91e-91FFCP PHASE1:Hg19::chr22:24828830..24828842,+#_d4a2c9ba061b51df18720df323a6968ap14@ADORA2A
4.91e-91FFCP PHASE2:Hg19::chr19:1236637..1236645,-#_d4a2c9ba061b51df18720df323a6968ap@chr19:1236637..1236645, -
4.91e-91FFCP PHASE1:Hg19::chr19:1236637..1236645,-#_d4a2c9ba061b51df18720df323a6968ap@chr19:1236637..1236645, -
4.91e-91FFCP PHASE1:Hg19::chr1:242372439..242372456,+#_d4a2c9ba061b51df18720df323a6968ap1@ENST00000421878
4.91e-91FFCP PHASE1:Hg19::chr11:26495467..26495474,+#_d4a2c9ba061b51df18720df323a6968ap8@ANO3
2.86e-89FFCP PHASE1:Hg19::chr11:67174819..67174825,-#_5ebc6196d37a09845db262a7883fd883p14@PPP1CA
2.86e-89FFCP PHASE2:Hg19::chr11:67174819..67174825,-#_5ebc6196d37a09845db262a7883fd883p14@PPP1CA
1.33e-87FFCP PHASE2:Hg19::chr17:19390234..19390251,+#_4c69a3fdadd8a4047ead6a1d2b121162p@chr17:19390234..19390251, +
1.33e-87FFCP PHASE1:Hg19::chr17:19390234..19390251,+#_4c69a3fdadd8a4047ead6a1d2b121162p@chr17:19390234..19390251, +
1.37e-87FFCP PHASE2:Hg19::chr8:25281776..25281779,-#_7b9575641cc9053363d6425c62ce6b1cp1@GNRH1
1.37e-87FFCP PHASE1:Hg19::chr1:31352916..31352926,-#_7b9575641cc9053363d6425c62ce6b1cp@chr1:31352916..31352926, -
1.37e-87FFCP PHASE2:Hg19::chr14:78638610..78638621,+#_7b9575641cc9053363d6425c62ce6b1cp@chr14:78638610..78638621, +
1.37e-87FFCP PHASE2:Hg19::chr2:152828264..152828299,-#_7b9575641cc9053363d6425c62ce6b1cp@chr2:152828264..152828299, -
1.37e-87FFCP PHASE2:Hg19::chr7:29846088..29846091,+#_7b9575641cc9053363d6425c62ce6b1cp20@WIPF3
1.37e-87FFCP PHASE1:Hg19::chr8:19799565..19799589,-#_7b9575641cc9053363d6425c62ce6b1cp@chr8:19799565..19799589, -
1.37e-87FFCP PHASE2:Hg19::chr18:47967428..47967437,-#_7b9575641cc9053363d6425c62ce6b1cp@chr18:47967428..47967437, -
1.37e-87FFCP PHASE1:Hg19::chr7:22382758..22382765,-#_7b9575641cc9053363d6425c62ce6b1cp@chr7:22382758..22382765, -
1.37e-87FFCP PHASE1:Hg19::chr18:47967428..47967437,-#_7b9575641cc9053363d6425c62ce6b1cp@chr18:47967428..47967437, -
1.37e-87FFCP PHASE1:Hg19::chr15:35546154..35546174,-#_7b9575641cc9053363d6425c62ce6b1cp@chr15:35546154..35546174, -
1.37e-87FFCP PHASE1:Hg19::chr7:29846088..29846091,+#_7b9575641cc9053363d6425c62ce6b1cp20@WIPF3
1.37e-87FFCP PHASE2:Hg19::chr7:22382758..22382765,-#_7b9575641cc9053363d6425c62ce6b1cp@chr7:22382758..22382765, -
1.37e-87FFCP PHASE1:Hg19::chr12:6031299..6031315,-#_7b9575641cc9053363d6425c62ce6b1cp@chr12:6031299..6031315, -
1.37e-87FFCP PHASE2:Hg19::chr1:31352916..31352926,-#_7b9575641cc9053363d6425c62ce6b1cp@chr1:31352916..31352926, -
1.37e-87FFCP PHASE1:Hg19::chr8:25281776..25281779,-#_7b9575641cc9053363d6425c62ce6b1cp1@GNRH1
1.37e-87FFCP PHASE2:Hg19::chr15:35546154..35546174,-#_7b9575641cc9053363d6425c62ce6b1cp@chr15:35546154..35546174, -
1.37e-87FFCP PHASE2:Hg19::chr12:6031299..6031315,-#_7b9575641cc9053363d6425c62ce6b1cp@chr12:6031299..6031315, -
1.37e-87FFCP PHASE2:Hg19::chr13:112726433..112726446,+#_7b9575641cc9053363d6425c62ce6b1cp@chr13:112726433..112726446, +
1.37e-87FFCP PHASE1:Hg19::chr14:78638610..78638621,+#_7b9575641cc9053363d6425c62ce6b1cp@chr14:78638610..78638621, +
1.37e-87FFCP PHASE1:Hg19::chr13:112726433..112726446,+#_7b9575641cc9053363d6425c62ce6b1cp@chr13:112726433..112726446, +
1.37e-87FFCP PHASE2:Hg19::chr8:19799565..19799589,-#_7b9575641cc9053363d6425c62ce6b1cp@chr8:19799565..19799589, -
1.37e-87FFCP PHASE1:Hg19::chr2:152828264..152828299,-#_7b9575641cc9053363d6425c62ce6b1cp@chr2:152828264..152828299, -
1.54e-87FFCP PHASE2:Hg19::chr3:35722978..35722999,+#_7ec133c70824cb99ca5808841e0933d0p28@ARPP21
1.54e-87FFCP PHASE1:Hg19::chr3:35722978..35722999,+#_7ec133c70824cb99ca5808841e0933d0p28@ARPP21
1.79e-87FFCP PHASE2:Hg19::chr11:26495447..26495461,+#_5f3f36ff654296dabfff207588bceb4ep5@ANO3
1.79e-87FFCP PHASE2:Hg19::chr10:73313437..73313451,-#_5f3f36ff654296dabfff207588bceb4ep@chr10:73313437..73313451, -
1.79e-87FFCP PHASE1:Hg19::chr10:73313437..73313451,-#_5f3f36ff654296dabfff207588bceb4ep@chr10:73313437..73313451, -
1.79e-87FFCP PHASE1:Hg19::chr11:26495447..26495461,+#_5f3f36ff654296dabfff207588bceb4ep5@ANO3
2.08e-87FFCP PHASE1:Hg19::chr3:16851273..16851310,+#_9c71161ffc47871cce059d92372c9de9p@chr3:16851273..16851310, +
2.08e-87FFCP PHASE2:Hg19::chr3:16851273..16851310,+#_9c71161ffc47871cce059d92372c9de9p@chr3:16851273..16851310, +
2.42e-87FFCP PHASE1:Hg19::chr14:78638636..78638661,+#_fc295f4455f3e89d7d5772498c34bfb3p@chr14:78638636..78638661, +
2.42e-87FFCP PHASE2:Hg19::chr7:67899920..67899958,-#_fc295f4455f3e89d7d5772498c34bfb3p@chr7:67899920..67899958, -
2.42e-87FFCP PHASE1:Hg19::chr7:67899920..67899958,-#_fc295f4455f3e89d7d5772498c34bfb3p@chr7:67899920..67899958, -
2.42e-87FFCP PHASE2:Hg19::chr14:78638636..78638661,+#_fc295f4455f3e89d7d5772498c34bfb3p@chr14:78638636..78638661, +
5.29e-79FFCP PHASE2:Hg19::chr6:166076645..166076657,-#_c83063ffa76d7084b249c43d9077a75fp@chr6:166076645..166076657, -
5.29e-79FFCP PHASE1:Hg19::chr6:166076645..166076657,-#_c83063ffa76d7084b249c43d9077a75fp@chr6:166076645..166076657, -
6.06e-79FFCP PHASE2:Hg19::chr11:18765589..18765610,-#_1da6aed881744eb183e1d08b0cbf9119p6@PTPN5
6.06e-79FFCP PHASE1:Hg19::chr22:27727719..27727726,+#_1da6aed881744eb183e1d08b0cbf9119p2@ENST00000413244
6.06e-79FFCP PHASE1:Hg19::chr11:18765589..18765610,-#_1da6aed881744eb183e1d08b0cbf9119p6@PTPN5
6.06e-79FFCP PHASE2:Hg19::chr22:27727719..27727726,+#_1da6aed881744eb183e1d08b0cbf9119p2@ENST00000413244
1.55e-78FFCP PHASE1:Hg19::chr21:43917191..43917207,-#_c8b3a4b33327a0ad7aaab10d30c189b1p@chr21:43917191..43917207, -
1.55e-78FFCP PHASE2:Hg19::chr21:43917191..43917207,-#_c8b3a4b33327a0ad7aaab10d30c189b1p@chr21:43917191..43917207, -
2.32e-78FFCP PHASE1:Hg19::chr5:75379091..75379100,+#_d8400f0e593a9052ab2437bfa6407d91p6@SV2C
2.32e-78FFCP PHASE2:Hg19::chr13:98995904..98995913,+#_d8400f0e593a9052ab2437bfa6407d91p@chr13:98995904..98995913, +
2.32e-78FFCP PHASE2:Hg19::chr6:80472250..80472261,+#_d8400f0e593a9052ab2437bfa6407d91p@chr6:80472250..80472261, +
2.32e-78FFCP PHASE1:Hg19::chr6:80472250..80472261,+#_d8400f0e593a9052ab2437bfa6407d91p@chr6:80472250..80472261, +
2.32e-78FFCP PHASE2:Hg19::chr5:75379091..75379100,+#_d8400f0e593a9052ab2437bfa6407d91p6@SV2C
2.32e-78FFCP PHASE1:Hg19::chr13:98995904..98995913,+#_d8400f0e593a9052ab2437bfa6407d91p@chr13:98995904..98995913, +
3.19e-78FFCP PHASE1:Hg19::chr11:80886203..80886231,+#_b816196914bd6bac5882fcbaa5fa7433p@chr11:80886203..80886231, +
3.19e-78FFCP PHASE1:Hg19::chr1:101003738..101003747,+#_b816196914bd6bac5882fcbaa5fa7433p9@GPR88
3.19e-78FFCP PHASE2:Hg19::chr1:101003738..101003747,+#_b816196914bd6bac5882fcbaa5fa7433p9@GPR88
3.19e-78FFCP PHASE1:Hg19::chrX:37765754..37765765,+#_b816196914bd6bac5882fcbaa5fa7433p11@ENST00000449263
3.19e-78FFCP PHASE2:Hg19::chrX:37765754..37765765,+#_b816196914bd6bac5882fcbaa5fa7433p11@ENST00000449263
3.19e-78FFCP PHASE2:Hg19::chr11:80886203..80886231,+#_b816196914bd6bac5882fcbaa5fa7433p@chr11:80886203..80886231, +
3.75e-78FFCP PHASE1:Hg19::chr5:79866189..79866202,+#_d5701389a9c5249e537df2088deff56dp@chr5:79866189..79866202, +
3.75e-78FFCP PHASE1:Hg19::chr20:9495125..9495132,+#_d5701389a9c5249e537df2088deff56dp17@LAMP5
3.75e-78FFCP PHASE2:Hg19::chr5:79866189..79866202,+#_d5701389a9c5249e537df2088deff56dp@chr5:79866189..79866202, +
3.75e-78FFCP PHASE2:Hg19::chr20:9495125..9495132,+#_d5701389a9c5249e537df2088deff56dp17@LAMP5
5.78e-72FFCP PHASE2:Hg19::chr12:122181551..122181562,+#_4d6eb6eda1174f29a5dc72d7b3e0a06cp@chr12:122181551..122181562, +
5.78e-72FFCP PHASE1:Hg19::chr12:122181551..122181562,+#_4d6eb6eda1174f29a5dc72d7b3e0a06cp@chr12:122181551..122181562, +
7.39e-72FFCP PHASE1:Hg19::chr11:120690389..120690422,+#_41b1c320e6f79224c8aae267061fb745p@chr11:120690389..120690422, +
7.39e-72FFCP PHASE2:Hg19::chr11:120690389..120690422,+#_41b1c320e6f79224c8aae267061fb745p@chr11:120690389..120690422, +
1.07e-71FFCP PHASE1:Hg19::chr14:78638668..78638680,+#_003d258a11bec356233a6a364f80dec2p@chr14:78638668..78638680, +
1.07e-71FFCP PHASE2:Hg19::chr14:78638668..78638680,+#_003d258a11bec356233a6a364f80dec2p@chr14:78638668..78638680, +
2.16e-70FFCP PHASE2:Hg19::chr2:127783377..127783391,+#_3c746f2986f2dc81d2c2fc26538f0df0p2@BC051739
2.16e-70FFCP PHASE1:Hg19::chr3:57807798..57807809,+#_3c746f2986f2dc81d2c2fc26538f0df0p@chr3:57807798..57807809, +
2.16e-70FFCP PHASE1:Hg19::chr10:97261874..97261887,-#_3c746f2986f2dc81d2c2fc26538f0df0p@chr10:97261874..97261887, -
2.16e-70FFCP PHASE2:Hg19::chr10:97261874..97261887,-#_3c746f2986f2dc81d2c2fc26538f0df0p@chr10:97261874..97261887, -
2.16e-70FFCP PHASE2:Hg19::chr20:9496091..9496106,+#_3c746f2986f2dc81d2c2fc26538f0df0p@chr20:9496091..9496106, +
2.16e-70FFCP PHASE2:Hg19::chr3:57807798..57807809,+#_3c746f2986f2dc81d2c2fc26538f0df0p@chr3:57807798..57807809, +

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