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{{UBERON
{{UBERON
|id=UBERON:0002420
|alt_id=
|name=basal ganglion
|namespace=
|def="one of a group of nuclei in the brains of vertebrates, situated at the base of the forebrain and strongly connected with the cerebral cortex, thalamus and other areas.ganglion in the head. The main components of the basal ganglia are the striatum, pallidum, substantia nigra, and subthalamic nucleus[WP]. Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF]." [Wikipedia:Basal_ganglia]
|xref=BTO:0000235;;EFO:0000904;;FMA:62514;;http://upload.wikimedia.org/wikipedia/commons/1/1b/Basal_Ganglia_and_Related_Structures.svg;;http://upload.wikimedia.org/wikipedia/commons/thumb/1/1b/Basal_Ganglia_and_Related_Structures.svg/200px-Basal_Ganglia_and_Related_Structures.svg.png;;SCTID:244434001
|is_a=UBERON:0003528;;UBERON:0007245
|synonym="basal ganglia" RELATED PLURAL [];;"basal ganglion of telencephalon" EXACT [];;"basal nucleus" RELATED [MA:0000184];;"nuclei basales" RELATED LATIN [Wikipedia:Basal_ganglia]
|comment=Editor note: it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular.  it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.
|comment=Editor note: it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular.  it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.
|alt_id=
|disjoint_from=
|union_of=
|created_by=
|created_by=
|obo_creation_date=
|def="one of a group of nuclei in the brains of vertebrates, situated at the base of the forebrain and strongly connected with the cerebral cortex, thalamus and other areas.ganglion in the head. The main components of the basal ganglia are the striatum, pallidum, substantia nigra, and subthalamic nucleus[WP]. Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF]." [Wikipedia:Basal_ganglia]
|subset=uberon_slim
|derives_from=
|derives_from=
|develops_from=
|develops_from=
|disjoint_from=
|has_quality=
|has_quality=
|id=UBERON:0002420
|is_a=UBERON:0003528 ;;UBERON:0007245
|is_obsolete=
|located_in=
|located_in=
|part_of=
|name=basal ganglion
|namespace=FANTOM
|obo_creation_date=
|part_of=UBERON:0010011
|preceded_by=
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|is_obsolete=
|subset=uberon_slim
|preceded_by=
|synonym="basal ganglia" RELATED PLURAL [];;"basal ganglion of telencephalon" EXACT [];;"basal nucleus" RELATED [MA:0000184];;"nuclei basales" RELATED LATIN [Wikipedia:Basal_ganglia]
|union_of=
|xref=BTO:0000235;;EFO:0000904;;FMA:62514;;http://upload.wikimedia.org/wikipedia/commons/1/1b/Basal_Ganglia_and_Related_Structures.svg;;http://upload.wikimedia.org/wikipedia/commons/thumb/1/1b/Basal_Ganglia_and_Related_Structures.svg/200px-Basal_Ganglia_and_Related_Structures.svg.png;;SCTID:244434001
}}
}}

Latest revision as of 17:32, 12 September 2014

Name:basal ganglion
Namespace:FANTOM
Definition:"one of a group of nuclei in the brains of vertebrates, situated at the base of the forebrain and strongly connected with the cerebral cortex, thalamus and other areas.ganglion in the head. The main components of the basal ganglia are the striatum, pallidum, substantia nigra, and subthalamic nucleus[WP]. Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF]." [Wikipedia:Basal_ganglia]
Xrefs:
links:

BTO:0000235
EFO:0000904
FMA:62514
[1]
[ 200px-Basal_Ganglia_and_Related_Structures.svg.png 200px-Basal_Ganglia_and_Related_Structures.svg.png]

SCTID:244434001
Synonyms: "basal ganglia" RELATED PLURAL []
"basal ganglion of telencephalon" EXACT []
"basal nucleus" RELATED [MA:0000184]
"nuclei basales" RELATED LATIN [Wikipedia:Basal_ganglia]
Comments:Editor note: it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.
Subset: uberon_slim

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:0003528(brain grey matter),UBERON:0007245(nuclear complex of neuraxis)
part_of:UBERON:0010011(collection of basal ganglia)



Children

is a:UBERON:0001876 (amygdala)
disjoint from:UBERON:0000045 (ganglion)
part of:UBERON:0000369 (corpus striatum),UBERON:0001875 (globus pallidus),UBERON:0002038 (substantia nigra),UBERON:0002435 (striatum),UBERON:0006514 (pallidum)

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:0002420 (basal ganglion), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

P-valueFFCPShort description
1.82e-133FFCP PHASE2:Hg19::chr18:11751466..11751475,+#_33a7146e9ea7259c3f7ed5ed1348f986p22@GNAL
1.82e-133FFCP PHASE1:Hg19::chr18:11751466..11751475,+#_33a7146e9ea7259c3f7ed5ed1348f986p22@GNAL
1.42e-130FFCP PHASE2:Hg19::chr15:40582949..40582989,+#_f4677b208efc021eb2b1c917568c9e17p@chr15:40582949..40582989, +
1.42e-130FFCP PHASE1:Hg19::chr15:40582949..40582989,+#_f4677b208efc021eb2b1c917568c9e17p@chr15:40582949..40582989, +
1.21e-118FFCP PHASE1:Hg19::chr3:35722978..35722999,+#_ffa6a53c377dcb8556b0efe765985091p28@ARPP21
1.21e-118FFCP PHASE2:Hg19::chr3:35722978..35722999,+#_ffa6a53c377dcb8556b0efe765985091p28@ARPP21
3.02e-112FFCP PHASE2:Hg19::chr13:98995904..98995913,+#_f7bee23e2c6b93a6d7a4997205ccef47p@chr13:98995904..98995913, +
3.02e-112FFCP PHASE1:Hg19::chr13:98995904..98995913,+#_f7bee23e2c6b93a6d7a4997205ccef47p@chr13:98995904..98995913, +
3.66e-112FFCP PHASE2:Hg19::chr11:80886203..80886231,+#_d342ba7996322e3ae1d0c4b0ccaba07fp@chr11:80886203..80886231, +
3.66e-112FFCP PHASE1:Hg19::chr11:80886203..80886231,+#_d342ba7996322e3ae1d0c4b0ccaba07fp@chr11:80886203..80886231, +
6.51e-112FFCP PHASE1:Hg19::chr2:7112752..7112770,+#_3c5d4b30ff4ceddb8370e689499bd00ep@chr2:7112752..7112770, +
6.51e-112FFCP PHASE2:Hg19::chr2:7112752..7112770,+#_3c5d4b30ff4ceddb8370e689499bd00ep@chr2:7112752..7112770, +
7.88e-112FFCP PHASE1:Hg19::chr22:27727810..27727817,+#_7aefbc2cc98d62d958439b99ee9e58cdp3@ENST00000413244
7.88e-112FFCP PHASE2:Hg19::chr22:27727810..27727817,+#_7aefbc2cc98d62d958439b99ee9e58cdp3@ENST00000413244
4.6e-109FFCP PHASE1:Hg19::chr15:35546024..35546035,-#_5abd4d46d5b7941e49b3d88324f36bfep@chr15:35546024..35546035, -
4.6e-109FFCP PHASE1:Hg19::chr2:3853961..3853984,+#_5abd4d46d5b7941e49b3d88324f36bfep@chr2:3853961..3853984, +
4.6e-109FFCP PHASE2:Hg19::chr15:35546024..35546035,-#_5abd4d46d5b7941e49b3d88324f36bfep@chr15:35546024..35546035, -
4.6e-109FFCP PHASE2:Hg19::chr2:3853961..3853984,+#_5abd4d46d5b7941e49b3d88324f36bfep@chr2:3853961..3853984, +
4.6e-109FFCP PHASE1:Hg19::chr17:19390211..19390223,+#_5abd4d46d5b7941e49b3d88324f36bfep@chr17:19390211..19390223, +
4.6e-109FFCP PHASE2:Hg19::chr19:719510..719520,+#_5abd4d46d5b7941e49b3d88324f36bfep@chr19:719510..719520, +
4.6e-109FFCP PHASE1:Hg19::chr19:719510..719520,+#_5abd4d46d5b7941e49b3d88324f36bfep@chr19:719510..719520, +
4.6e-109FFCP PHASE2:Hg19::chr17:19390211..19390223,+#_5abd4d46d5b7941e49b3d88324f36bfep@chr17:19390211..19390223, +
4.01e-107FFCP PHASE1:Hg19::chr18:11751516..11751523,+#_2079a443988c134edc8481670e8fa2d5p17@GNAL
4.01e-107FFCP PHASE2:Hg19::chr18:11751516..11751523,+#_2079a443988c134edc8481670e8fa2d5p17@GNAL
1.41e-106FFCP PHASE1:Hg19::chr21:43917191..43917207,-#_590bb6449e94fd560014a8629c2dc31dp@chr21:43917191..43917207, -
1.41e-106FFCP PHASE2:Hg19::chr21:43917191..43917207,-#_590bb6449e94fd560014a8629c2dc31dp@chr21:43917191..43917207, -
3.33e-98FFCP PHASE2:Hg19::chr11:18765839..18765846,-#_6cf85cc3bc59ceb92a64b3a0548a6820p10@PTPN5
3.33e-98FFCP PHASE1:Hg19::chr11:18765839..18765846,-#_6cf85cc3bc59ceb92a64b3a0548a6820p10@PTPN5
1.43e-97FFCP PHASE2:Hg19::chr13:98995923..98995941,+#_0eeb99c16e82f8fdb47caba6a2fefffap@chr13:98995923..98995941, +
1.43e-97FFCP PHASE1:Hg19::chr13:98995923..98995941,+#_0eeb99c16e82f8fdb47caba6a2fefffap@chr13:98995923..98995941, +
4.08e-91FFCP PHASE1:Hg19::chr11:26497871..26497889,+#_45c9707ae9427530a417bf8a5a3f6244p@chr11:26497871..26497889, +
4.08e-91FFCP PHASE2:Hg19::chr11:26497871..26497889,+#_45c9707ae9427530a417bf8a5a3f6244p@chr11:26497871..26497889, +
4.08e-91FFCP PHASE2:Hg19::chr10:97261901..97261919,-#_45c9707ae9427530a417bf8a5a3f6244p@chr10:97261901..97261919, -
4.08e-91FFCP PHASE1:Hg19::chr10:97261901..97261919,-#_45c9707ae9427530a417bf8a5a3f6244p@chr10:97261901..97261919, -
4.91e-91FFCP PHASE2:Hg19::chr1:242372439..242372456,+#_4c3ad772a4fb082c20de4cf7183266c6p1@ENST00000421878
4.91e-91FFCP PHASE2:Hg19::chr22:24828830..24828842,+#_4c3ad772a4fb082c20de4cf7183266c6p14@ADORA2A
4.91e-91FFCP PHASE1:Hg19::chr1:242372439..242372456,+#_4c3ad772a4fb082c20de4cf7183266c6p1@ENST00000421878
4.91e-91FFCP PHASE2:Hg19::chr19:1236637..1236645,-#_4c3ad772a4fb082c20de4cf7183266c6p@chr19:1236637..1236645, -
4.91e-91FFCP PHASE1:Hg19::chr11:26495467..26495474,+#_4c3ad772a4fb082c20de4cf7183266c6p8@ANO3
4.91e-91FFCP PHASE1:Hg19::chr22:24828830..24828842,+#_4c3ad772a4fb082c20de4cf7183266c6p14@ADORA2A
4.91e-91FFCP PHASE1:Hg19::chr19:1236637..1236645,-#_4c3ad772a4fb082c20de4cf7183266c6p@chr19:1236637..1236645, -
4.91e-91FFCP PHASE2:Hg19::chr11:26495467..26495474,+#_4c3ad772a4fb082c20de4cf7183266c6p8@ANO3
1.7e-89FFCP PHASE1:Hg19::chr11:18765553..18765567,-#_7475fa41c06a49e0a248306bab3bdf5fp7@PTPN5
1.7e-89FFCP PHASE2:Hg19::chr1:174417095..174417131,+#_7475fa41c06a49e0a248306bab3bdf5fp1@GPR52
1.7e-89FFCP PHASE1:Hg19::chr1:174417095..174417131,+#_7475fa41c06a49e0a248306bab3bdf5fp1@GPR52
1.7e-89FFCP PHASE2:Hg19::chr11:18765553..18765567,-#_7475fa41c06a49e0a248306bab3bdf5fp7@PTPN5
2.51e-89FFCP PHASE1:Hg19::chr1:101003675..101003682,+#_56f9538612ff16306ebed8b9523c18bep5@GPR88
2.51e-89FFCP PHASE2:Hg19::chr1:101003675..101003682,+#_56f9538612ff16306ebed8b9523c18bep5@GPR88
2.86e-89FFCP PHASE1:Hg19::chr11:67174819..67174825,-#_ba0e6f5d4cc9bd72af10c4cb6ebbc87cp14@PPP1CA
2.86e-89FFCP PHASE2:Hg19::chr11:67174819..67174825,-#_ba0e6f5d4cc9bd72af10c4cb6ebbc87cp14@PPP1CA
4.81e-88FFCP PHASE2:Hg19::chr11:18765881..18765897,-#_3ba21d830c894798f063f956cc93bf1bp3@PTPN5
4.81e-88FFCP PHASE1:Hg19::chr11:18765881..18765897,-#_3ba21d830c894798f063f956cc93bf1bp3@PTPN5
1.33e-87FFCP PHASE1:Hg19::chr17:19390234..19390251,+#_2875fbdfa0482a1f33c78c9ea6cdfab2p@chr17:19390234..19390251, +
1.33e-87FFCP PHASE2:Hg19::chr17:19390234..19390251,+#_2875fbdfa0482a1f33c78c9ea6cdfab2p@chr17:19390234..19390251, +
1.37e-87FFCP PHASE2:Hg19::chr13:112726433..112726446,+#_aba7d6813a519648a9a499b98324ef5ep@chr13:112726433..112726446, +
1.37e-87FFCP PHASE1:Hg19::chr14:78638610..78638621,+#_aba7d6813a519648a9a499b98324ef5ep@chr14:78638610..78638621, +
1.37e-87FFCP PHASE1:Hg19::chr15:35546154..35546174,-#_aba7d6813a519648a9a499b98324ef5ep@chr15:35546154..35546174, -
1.37e-87FFCP PHASE2:Hg19::chr8:25281776..25281779,-#_aba7d6813a519648a9a499b98324ef5ep1@GNRH1
1.37e-87FFCP PHASE1:Hg19::chr7:22382758..22382765,-#_aba7d6813a519648a9a499b98324ef5ep@chr7:22382758..22382765, -
1.37e-87FFCP PHASE1:Hg19::chr2:152828264..152828299,-#_aba7d6813a519648a9a499b98324ef5ep@chr2:152828264..152828299, -
1.37e-87FFCP PHASE1:Hg19::chr7:29846088..29846091,+#_aba7d6813a519648a9a499b98324ef5ep20@WIPF3
1.37e-87FFCP PHASE1:Hg19::chr18:47967428..47967437,-#_aba7d6813a519648a9a499b98324ef5ep@chr18:47967428..47967437, -
1.37e-87FFCP PHASE2:Hg19::chr18:47967428..47967437,-#_aba7d6813a519648a9a499b98324ef5ep@chr18:47967428..47967437, -
1.37e-87FFCP PHASE1:Hg19::chr1:31352916..31352926,-#_aba7d6813a519648a9a499b98324ef5ep@chr1:31352916..31352926, -
1.37e-87FFCP PHASE1:Hg19::chr8:25281776..25281779,-#_aba7d6813a519648a9a499b98324ef5ep1@GNRH1
1.37e-87FFCP PHASE2:Hg19::chr7:22382758..22382765,-#_aba7d6813a519648a9a499b98324ef5ep@chr7:22382758..22382765, -
1.37e-87FFCP PHASE2:Hg19::chr12:6031299..6031315,-#_aba7d6813a519648a9a499b98324ef5ep@chr12:6031299..6031315, -
1.37e-87FFCP PHASE2:Hg19::chr8:19799565..19799589,-#_aba7d6813a519648a9a499b98324ef5ep@chr8:19799565..19799589, -
1.37e-87FFCP PHASE1:Hg19::chr8:19799565..19799589,-#_aba7d6813a519648a9a499b98324ef5ep@chr8:19799565..19799589, -
1.37e-87FFCP PHASE2:Hg19::chr15:35546154..35546174,-#_aba7d6813a519648a9a499b98324ef5ep@chr15:35546154..35546174, -
1.37e-87FFCP PHASE2:Hg19::chr1:31352916..31352926,-#_aba7d6813a519648a9a499b98324ef5ep@chr1:31352916..31352926, -
1.37e-87FFCP PHASE2:Hg19::chr14:78638610..78638621,+#_aba7d6813a519648a9a499b98324ef5ep@chr14:78638610..78638621, +
1.37e-87FFCP PHASE2:Hg19::chr2:152828264..152828299,-#_aba7d6813a519648a9a499b98324ef5ep@chr2:152828264..152828299, -
1.37e-87FFCP PHASE1:Hg19::chr13:112726433..112726446,+#_aba7d6813a519648a9a499b98324ef5ep@chr13:112726433..112726446, +
1.37e-87FFCP PHASE1:Hg19::chr12:6031299..6031315,-#_aba7d6813a519648a9a499b98324ef5ep@chr12:6031299..6031315, -
1.37e-87FFCP PHASE2:Hg19::chr7:29846088..29846091,+#_aba7d6813a519648a9a499b98324ef5ep20@WIPF3
1.79e-87FFCP PHASE2:Hg19::chr11:26495447..26495461,+#_a46880773fa7e87974581a7b38200b6ep5@ANO3
1.79e-87FFCP PHASE1:Hg19::chr10:73313437..73313451,-#_a46880773fa7e87974581a7b38200b6ep@chr10:73313437..73313451, -
1.79e-87FFCP PHASE2:Hg19::chr10:73313437..73313451,-#_a46880773fa7e87974581a7b38200b6ep@chr10:73313437..73313451, -
1.79e-87FFCP PHASE1:Hg19::chr11:26495447..26495461,+#_a46880773fa7e87974581a7b38200b6ep5@ANO3
2.08e-87FFCP PHASE1:Hg19::chr3:16851273..16851310,+#_ffb4fbcc8c830da04552462bc69e2451p@chr3:16851273..16851310, +
2.08e-87FFCP PHASE2:Hg19::chr3:16851273..16851310,+#_ffb4fbcc8c830da04552462bc69e2451p@chr3:16851273..16851310, +
2.42e-87FFCP PHASE1:Hg19::chr7:67899920..67899958,-#_70b96ca037eb59b96a0dd3f6d8623e25p@chr7:67899920..67899958, -
2.42e-87FFCP PHASE2:Hg19::chr7:67899920..67899958,-#_70b96ca037eb59b96a0dd3f6d8623e25p@chr7:67899920..67899958, -
2.8e-87FFCP PHASE2:Hg19::chr9:95569585..95569596,+#_a532729e1c9bc5acc552022145d5e649p@chr9:95569585..95569596, +
2.8e-87FFCP PHASE1:Hg19::chr9:95569585..95569596,+#_a532729e1c9bc5acc552022145d5e649p@chr9:95569585..95569596, +
4.39e-83FFCP PHASE2:Hg19::chr18:11751493..11751507,+#_8413f3cdc603672a2448a1a9229c2b40p12@GNAL
4.39e-83FFCP PHASE1:Hg19::chr18:11751493..11751507,+#_8413f3cdc603672a2448a1a9229c2b40p12@GNAL
3.09e-79FFCP PHASE1:Hg19::chr11:13461601..13461620,-#_d9d3d149bfc0683996464679cf7886e6p5@BTBD10
3.09e-79FFCP PHASE2:Hg19::chr11:13461601..13461620,-#_d9d3d149bfc0683996464679cf7886e6p5@BTBD10
5.29e-79FFCP PHASE2:Hg19::chr6:166076645..166076657,-#_1bbac9997a592dda9651407dbf5a113fp@chr6:166076645..166076657, -
5.29e-79FFCP PHASE1:Hg19::chr6:166076645..166076657,-#_1bbac9997a592dda9651407dbf5a113fp@chr6:166076645..166076657, -
6.06e-79FFCP PHASE2:Hg19::chr2:26781521..26781537,-#_d558b8144727cfe2d7f53059663d1b29p2@OTOF
6.06e-79FFCP PHASE1:Hg19::chr22:27727719..27727726,+#_d558b8144727cfe2d7f53059663d1b29p2@ENST00000413244
6.06e-79FFCP PHASE2:Hg19::chr11:18765589..18765610,-#_d558b8144727cfe2d7f53059663d1b29p6@PTPN5
6.06e-79FFCP PHASE2:Hg19::chr22:27727719..27727726,+#_d558b8144727cfe2d7f53059663d1b29p2@ENST00000413244
6.06e-79FFCP PHASE1:Hg19::chr2:26781521..26781537,-#_d558b8144727cfe2d7f53059663d1b29p2@OTOF
6.06e-79FFCP PHASE1:Hg19::chr11:18765589..18765610,-#_d558b8144727cfe2d7f53059663d1b29p6@PTPN5
6.93e-79FFCP PHASE2:Hg19::chr19:19640188..19640201,+#_1b1697d6c4208af85475c93288887376p@chr19:19640188..19640201, +
6.93e-79FFCP PHASE1:Hg19::chr19:19640188..19640201,+#_1b1697d6c4208af85475c93288887376p@chr19:19640188..19640201, +

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