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UBERON:0000125

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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
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.

link to ontology dataset
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


FF samples
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
Analyst: Hideya Kawaji

link to source dataset
human : data
mouse : data


P-valueFFCPShort description
6.51e-112FFCP PHASE1:Hg19::chr2:7112752..7112770,+#_02a34646a603f9b7b12a630daf3edbc2p@chr2:7112752..7112770, +
6.51e-112FFCP PHASE2:Hg19::chr2:7112752..7112770,+#_02a34646a603f9b7b12a630daf3edbc2p@chr2:7112752..7112770, +
7.88e-112FFCP PHASE1:Hg19::chr22:27727810..27727817,+#_df047eec61dba902e91f9f705026b181p3@ENST00000413244
7.88e-112FFCP PHASE2:Hg19::chr22:27727810..27727817,+#_df047eec61dba902e91f9f705026b181p3@ENST00000413244
4.6e-109FFCP PHASE2:Hg19::chr15:35546024..35546035,-#_d23b414bfac5ec82116a13a1b9b60986p@chr15:35546024..35546035, -
4.6e-109FFCP PHASE2:Hg19::chr17:19390211..19390223,+#_d23b414bfac5ec82116a13a1b9b60986p@chr17:19390211..19390223, +
4.6e-109FFCP PHASE1:Hg19::chr2:3853961..3853984,+#_d23b414bfac5ec82116a13a1b9b60986p@chr2:3853961..3853984, +
4.6e-109FFCP PHASE1:Hg19::chr15:35546024..35546035,-#_d23b414bfac5ec82116a13a1b9b60986p@chr15:35546024..35546035, -
4.6e-109FFCP PHASE1:Hg19::chr17:19390211..19390223,+#_d23b414bfac5ec82116a13a1b9b60986p@chr17:19390211..19390223, +
4.6e-109FFCP PHASE2: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 PHASE1:Hg19::chr11:18765839..18765846,-#_586cf29d8b306b3acf7697f8f8f15980p10@PTPN5
3.33e-98FFCP PHASE2:Hg19::chr11:18765839..18765846,-#_586cf29d8b306b3acf7697f8f8f15980p10@PTPN5
4.08e-91FFCP PHASE2:Hg19::chr10:97261901..97261919,-#_8a0831d3aefef1a8bcce8eba3978a925p@chr10:97261901..97261919, -
4.08e-91FFCP PHASE2:Hg19::chr11:26497871..26497889,+#_8a0831d3aefef1a8bcce8eba3978a925p@chr11:26497871..26497889, +
4.08e-91FFCP PHASE1:Hg19::chr10:97261901..97261919,-#_8a0831d3aefef1a8bcce8eba3978a925p@chr10:97261901..97261919, -
4.08e-91FFCP PHASE1:Hg19::chr11:26497871..26497889,+#_8a0831d3aefef1a8bcce8eba3978a925p@chr11:26497871..26497889, +
4.91e-91FFCP PHASE1:Hg19::chr11:26495467..26495474,+#_d4a2c9ba061b51df18720df323a6968ap8@ANO3
4.91e-91FFCP PHASE1:Hg19::chr1:242372439..242372456,+#_d4a2c9ba061b51df18720df323a6968ap1@ENST00000421878
4.91e-91FFCP PHASE1:Hg19::chr22:24828830..24828842,+#_d4a2c9ba061b51df18720df323a6968ap14@ADORA2A
4.91e-91FFCP PHASE1:Hg19::chr19:1236637..1236645,-#_d4a2c9ba061b51df18720df323a6968ap@chr19:1236637..1236645, -
4.91e-91FFCP PHASE2:Hg19::chr11:26495467..26495474,+#_d4a2c9ba061b51df18720df323a6968ap8@ANO3
4.91e-91FFCP PHASE2:Hg19::chr22:24828830..24828842,+#_d4a2c9ba061b51df18720df323a6968ap14@ADORA2A
4.91e-91FFCP PHASE2:Hg19::chr19:1236637..1236645,-#_d4a2c9ba061b51df18720df323a6968ap@chr19:1236637..1236645, -
4.91e-91FFCP PHASE2:Hg19::chr1:242372439..242372456,+#_d4a2c9ba061b51df18720df323a6968ap1@ENST00000421878
2.86e-89FFCP PHASE2:Hg19::chr11:67174819..67174825,-#_5ebc6196d37a09845db262a7883fd883p14@PPP1CA
2.86e-89FFCP PHASE1:Hg19::chr11:67174819..67174825,-#_5ebc6196d37a09845db262a7883fd883p14@PPP1CA
1.33e-87FFCP PHASE1:Hg19::chr17:19390234..19390251,+#_4c69a3fdadd8a4047ead6a1d2b121162+, p@chr17:19390234..19390251
1.33e-87FFCP PHASE2:Hg19::chr17:19390234..19390251,+#_4c69a3fdadd8a4047ead6a1d2b121162p@chr17:19390234..19390251, +
1.37e-87FFCP PHASE2:Hg19::chr18:47967428..47967437,-#_7b9575641cc9053363d6425c62ce6b1cp@chr18:47967428..47967437, -
1.37e-87FFCP PHASE1:Hg19::chr8:19799565..19799589,-#_7b9575641cc9053363d6425c62ce6b1c-, p@chr8:19799565..19799589
1.37e-87FFCP PHASE1:Hg19::chr8:25281776..25281779,-#_7b9575641cc9053363d6425c62ce6b1cp1@GNRH1
1.37e-87FFCP PHASE2:Hg19::chr14:78638610..78638621,+#_7b9575641cc9053363d6425c62ce6b1cp@chr14:78638610..78638621, +
1.37e-87FFCP PHASE2:Hg19::chr15:35546154..35546174,-#_7b9575641cc9053363d6425c62ce6b1cp@chr15:35546154..35546174, -
1.37e-87FFCP PHASE2:Hg19::chr2:152828264..152828299,-#_7b9575641cc9053363d6425c62ce6b1cp@chr2:152828264..152828299, -
1.37e-87FFCP PHASE2:Hg19::chr8:19799565..19799589,-#_7b9575641cc9053363d6425c62ce6b1cp@chr8:19799565..19799589, -
1.37e-87FFCP PHASE2:Hg19::chr8:25281776..25281779,-#_7b9575641cc9053363d6425c62ce6b1cp1@GNRH1
1.37e-87FFCP PHASE2:Hg19::chr1:31352916..31352926,-#_7b9575641cc9053363d6425c62ce6b1cp@chr1:31352916..31352926, -
1.37e-87FFCP PHASE2:Hg19::chr7:22382758..22382765,-#_7b9575641cc9053363d6425c62ce6b1cp@chr7:22382758..22382765, -
1.37e-87FFCP PHASE2:Hg19::chr7:29846088..29846091,+#_7b9575641cc9053363d6425c62ce6b1cp20@WIPF3
1.37e-87FFCP PHASE1: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::chr15:35546154..35546174,-#_7b9575641cc9053363d6425c62ce6b1cp@chr15:35546154..35546174, -
1.37e-87FFCP PHASE1: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::chr7:29846088..29846091,+#_7b9575641cc9053363d6425c62ce6b1cp20@WIPF3
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::chr12:6031299..6031315,-#_7b9575641cc9053363d6425c62ce6b1cp@chr12:6031299..6031315, -
1.37e-87FFCP PHASE1:Hg19::chr1:31352916..31352926,-#_7b9575641cc9053363d6425c62ce6b1cp@chr1:31352916..31352926, -
1.37e-87FFCP PHASE1:Hg19::chr2:152828264..152828299,-#_7b9575641cc9053363d6425c62ce6b1cp@chr2:152828264..152828299, -
1.54e-87FFCP PHASE1:Hg19::chr3:35722978..35722999,+#_7ec133c70824cb99ca5808841e0933d0p28@ARPP21
1.54e-87FFCP PHASE2:Hg19::chr3:35722978..35722999,+#_7ec133c70824cb99ca5808841e0933d0p28@ARPP21
1.79e-87FFCP PHASE2:Hg19::chr10:73313437..73313451,-#_5f3f36ff654296dabfff207588bceb4ep@chr10:73313437..73313451, -
1.79e-87FFCP PHASE2:Hg19::chr11:26495447..26495461,+#_5f3f36ff654296dabfff207588bceb4ep5@ANO3
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 PHASE2: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::chr14:78638636..78638661,+#_fc295f4455f3e89d7d5772498c34bfb3p@chr14:78638636..78638661, +
2.42e-87FFCP PHASE1:Hg19::chr7:67899920..67899958,-#_fc295f4455f3e89d7d5772498c34bfb3p@chr7:67899920..67899958, -
5.29e-79FFCP PHASE1:Hg19::chr6:166076645..166076657,-#_c83063ffa76d7084b249c43d9077a75fp@chr6:166076645..166076657, -
5.29e-79FFCP PHASE2:Hg19::chr6:166076645..166076657,-#_c83063ffa76d7084b249c43d9077a75fp@chr6:166076645..166076657, -
6.06e-79FFCP PHASE2:Hg19::chr22:27727719..27727726,+#_1da6aed881744eb183e1d08b0cbf9119p2@ENST00000413244
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
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 PHASE2:Hg19::chr6:80472250..80472261,+#_d8400f0e593a9052ab2437bfa6407d91p@chr6:80472250..80472261, +
2.32e-78FFCP PHASE2:Hg19::chr13:98995904..98995913,+#_d8400f0e593a9052ab2437bfa6407d91p@chr13:98995904..98995913, +
2.32e-78FFCP PHASE2:Hg19::chr5:75379091..75379100,+#_d8400f0e593a9052ab2437bfa6407d91p6@SV2C
2.32e-78FFCP PHASE1:Hg19::chr5:75379091..75379100,+#_d8400f0e593a9052ab2437bfa6407d91p6@SV2C
2.32e-78FFCP PHASE1:Hg19::chr6:80472250..80472261,+#_d8400f0e593a9052ab2437bfa6407d91p@chr6:80472250..80472261, +
2.32e-78FFCP PHASE1:Hg19::chr13:98995904..98995913,+#_d8400f0e593a9052ab2437bfa6407d91p@chr13:98995904..98995913, +
3.19e-78FFCP PHASE1:Hg19::chr1:101003738..101003747,+#_b816196914bd6bac5882fcbaa5fa7433p9@GPR88
3.19e-78FFCP PHASE1:Hg19::chr11:80886203..80886231,+#_b816196914bd6bac5882fcbaa5fa7433p@chr11:80886203..80886231, +
3.19e-78FFCP PHASE2:Hg19::chrX:37765754..37765765,+#_b816196914bd6bac5882fcbaa5fa7433p11@ENST00000449263
3.19e-78FFCP PHASE2:Hg19::chr11:80886203..80886231,+#_b816196914bd6bac5882fcbaa5fa7433p@chr11:80886203..80886231, +
3.19e-78FFCP PHASE2:Hg19::chr1:101003738..101003747,+#_b816196914bd6bac5882fcbaa5fa7433p9@GPR88
3.19e-78FFCP PHASE1:Hg19::chrX:37765754..37765765,+#_b816196914bd6bac5882fcbaa5fa7433p11@ENST00000449263
3.75e-78FFCP PHASE2:Hg19::chr5:79866189..79866202,+#_d5701389a9c5249e537df2088deff56dp@chr5:79866189..79866202, +
3.75e-78FFCP PHASE2:Hg19::chr20:9495125..9495132,+#_d5701389a9c5249e537df2088deff56dp17@LAMP5
3.75e-78FFCP PHASE1:Hg19::chr20:9495125..9495132,+#_d5701389a9c5249e537df2088deff56dp17@LAMP5
3.75e-78FFCP PHASE1:Hg19::chr5:79866189..79866202,+#_d5701389a9c5249e537df2088deff56dp@chr5:79866189..79866202, +
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 PHASE2:Hg19::chr14:78638668..78638680,+#_003d258a11bec356233a6a364f80dec2p@chr14:78638668..78638680, +
1.07e-71FFCP PHASE1:Hg19::chr14:78638668..78638680,+#_003d258a11bec356233a6a364f80dec2p@chr14:78638668..78638680, +
2.16e-70FFCP PHASE1:Hg19::chr10:97261874..97261887,-#_3c746f2986f2dc81d2c2fc26538f0df0p@chr10:97261874..97261887, -
2.16e-70FFCP PHASE1:Hg19::chr12:11652913..11652927,+#_3c746f2986f2dc81d2c2fc26538f0df0p@chr12:11652913..11652927, +
2.16e-70FFCP PHASE1:Hg19::chr3:57807798..57807809,+#_3c746f2986f2dc81d2c2fc26538f0df0+, p@chr3:57807798..57807809
2.16e-70FFCP PHASE2:Hg19::chr12:11652913..11652927,+#_3c746f2986f2dc81d2c2fc26538f0df0p@chr12:11652913..11652927, +
2.16e-70FFCP PHASE1:Hg19::chr20:9496091..9496106,+#_3c746f2986f2dc81d2c2fc26538f0df0p@chr20:9496091..9496106, +
2.16e-70FFCP PHASE1:Hg19::chr2:127783377..127783391,+#_3c746f2986f2dc81d2c2fc26538f0df0p2@BC051739