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{{UBERON
{{UBERON
|id=UBERON:0002298
|alt_id=UBERON:FMA_79876-MA_0000169
|name=brainstem
|anatomical_img_id=FMA:79876
|namespace=
|def="Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted]." [ISBN10:0471888893, Wikipedia:Brainstem, ZFA:0001707]
|xref=ABA:BS;;BTO:0000146;;EFO:0001962;;EV:0100241;;FMA:79876;;http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png;;http://upload.wikimedia.org/wikipedia/commons/thumb/b/b7/Gray719.png/200px-Gray719.png;;MA:0000169;;MESH:A.08.186.211.132;;ncithesaurus:Brain_Stem;;NIF_GrossAnatomy:birnlex_1565;;SCTID:180925009;;TAO:0002156;;VHOG:0001457;;ZFA:0001707
|is_a=UBERON:0002616;;UBERON:0010314
|synonym="brain stem" EXACT [ABA:BS];;"truncus encephali" EXACT LATIN [Wikipedia:Brainstem];;"truncus encephalicus" RELATED [BTO:0000146]
|comment='brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
|comment='brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
|alt_id=UBERON:FMA_79876-MA_0000169
|disjoint_from=
|union_of=
|created_by=
|created_by=
|obo_creation_date=
|def="Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted]." [ISBN10:0471888893, Wikipedia:Brainstem, ZFA:0001707]
|subset=loose_concept;;uberon_slim;;vertebrate_core
|derives_from=
|derives_from=
|develops_from=
|develops_from=
|disjoint_from=
|has_quality=
|has_quality=
|id=UBERON:0002298
|is_a=UBERON:0002616;;UBERON:0010314
|is_obsolete=
|located_in=
|located_in=
|name=brainstem
|namespace=
|obo_creation_date=
|part_of=UBERON:0000955
|part_of=UBERON:0000955
|preceded_by=
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl;;"spatially_disjoint_from" UBERON:0001890;;"spatially_disjoint_from" UBERON:0002037;;"spatially_disjoint_from" UBERON:0002314;;UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" xsd:string
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl;;"spatially_disjoint_from" UBERON:0001890;;"spatially_disjoint_from" UBERON:0002037;;"spatially_disjoint_from" UBERON:0002314;;UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" xsd:string
|is_obsolete=
|subset=loose_concept;;uberon_slim;;vertebrate_core
|preceded_by=
|synonym="brain stem" EXACT [ABA:BS];;"truncus encephali" EXACT LATIN [Wikipedia:Brainstem];;"truncus encephalicus" RELATED [BTO:0000146]
|union_of=
|xref=ABA:BS;;BTO:0000146;;EFO:0001962;;EV:0100241;;FMA:79876;;http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png;;http://upload.wikimedia.org/wikipedia/commons/thumb/b/b7/Gray719.png/200px-Gray719.png;;MA:0000169;;MESH:A.08.186.211.132;;ncithesaurus:Brain_Stem;;NIF_GrossAnatomy:birnlex_1565;;SCTID:180925009;;TAO:0002156;;VHOG:0001457;;ZFA:0001707
}}
}}

Revision as of 18:42, 29 November 2012

Name:brainstem
Definition:"Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted]." [ISBN10:0471888893, Wikipedia:Brainstem, ZFA:0001707]
Xrefs:
links:

ABA:BS
BTO:0000146
EFO:0001962
EV:0100241
FMA:79876
[ Gray719.png Gray719.png]
[ 200px-Gray719.png 200px-Gray719.png]
MA:0000169
MESH:A.08.186.211.132
ncithesaurus:Brain_Stem
NIF_GrossAnatomy:birnlex_1565
SCTID:180925009
TAO:0002156
VHOG:0001457

ZFA:0001707
Synonyms: "brain stem" EXACT [ABA:BS]
"truncus encephali" EXACT LATIN [Wikipedia:Brainstem]
"truncus encephalicus" RELATED [BTO:0000146]
Comments:'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
Alt_id: UBERON:FMA_79876-MA_0000169
Subset: loose_concept
uberon_slim
vertebrate_core

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:0002616(regional part of brain),UBERON:0010314(structure with developmental contribution from neural crest)
part_of:UBERON:0000955(brain)



Children

part of:UBERON:0000988 (pons),UBERON:0001896 (medulla oblongata),UBERON:0002275 (reticular formation),UBERON:0006331 (brainstem nucleus),UBERON:0015827 (brainstem reticular formation)

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:0002298 (brainstem), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

P-valueFFCPShort description
1.73e-118FFCP PHASE2:Hg19::chr12:72332618..72332632,+#_d66ad30c28141a4c845f221a2986ef7dp1@TPH2
1.73e-118FFCP PHASE1:Hg19::chr12:72332618..72332632,+#_d66ad30c28141a4c845f221a2986ef7dp1@TPH2
8.05e-117FFCP PHASE2:Hg19::chr4:117675601..117675614,+#_26af8d56ec17fc966bdd14c58c12aad5p@chr4:117675601..117675614, +
8.05e-117FFCP PHASE1:Hg19::chr4:117675601..117675614,+#_26af8d56ec17fc966bdd14c58c12aad5p@chr4:117675601..117675614, +
1.65e-116FFCP PHASE2:Hg19::chr2:69741832..69741847,-#_1ce75deb9f06e2af9d3128d156b22e91p@chr2:69741832..69741847, -
1.65e-116FFCP PHASE1:Hg19::chr2:69741832..69741847,-#_1ce75deb9f06e2af9d3128d156b22e91p@chr2:69741832..69741847, -
5.07e-102FFCP PHASE2:Hg19::chr9:128998376..128998387,-#_8f494f2b182dd0c1aae0f2bae2018a44p@chr9:128998376..128998387, -
5.07e-102FFCP PHASE1:Hg19::chr9:128998376..128998387,-#_8f494f2b182dd0c1aae0f2bae2018a44p@chr9:128998376..128998387, -
1.57e-98FFCP PHASE2:Hg19::chr2:72381655..72381673,-#_bea5de2b5ee97e65a786fdea7453c81ep@chr2:72381655..72381673, -
1.57e-98FFCP PHASE1:Hg19::chr2:72381655..72381673,-#_bea5de2b5ee97e65a786fdea7453c81ep@chr2:72381655..72381673, -
1.83e-98FFCP PHASE1:Hg19::chr5:126959224..126959239,+#_c04181094e2512171daa4dd2b2cfbb3cp@chr5:126959224..126959239, +
1.83e-98FFCP PHASE1:Hg19::chr16:49670005..49670020,-#_c04181094e2512171daa4dd2b2cfbb3cp@chr16:49670005..49670020, -
1.83e-98FFCP PHASE2:Hg19::chr5:126959224..126959239,+#_c04181094e2512171daa4dd2b2cfbb3cp@chr5:126959224..126959239, +
1.83e-98FFCP PHASE2:Hg19::chr16:49670005..49670020,-#_c04181094e2512171daa4dd2b2cfbb3cp@chr16:49670005..49670020, -
3.65e-98FFCP PHASE2:Hg19::chr16:290098..290109,+#_813d16cf0267b3f104241a123c3f51d6p13@ITFG3
3.65e-98FFCP PHASE1:Hg19::chr16:290098..290109,+#_813d16cf0267b3f104241a123c3f51d6p13@ITFG3
3.09e-91FFCP PHASE1:Hg19::chr11:20621148..20621166,+#_8178043de3e7d98d976ba929467e07d8p1@SLC6A5
3.09e-91FFCP PHASE2:Hg19::chr11:20621148..20621166,+#_8178043de3e7d98d976ba929467e07d8p1@SLC6A5
3.09e-91FFCP PHASE1:Hg19::chr15:60296481..60296492,+#_8178043de3e7d98d976ba929467e07d8p7@FOXB1
3.09e-91FFCP PHASE2:Hg19::chr15:60296481..60296492,+#_8178043de3e7d98d976ba929467e07d8p7@FOXB1
8.11e-91FFCP PHASE1:Hg19::chr15:79356984..79356998,-#_e97dcfb1b68795538757ef2464230176p8@RASGRF1
8.11e-91FFCP PHASE2:Hg19::chr15:79356984..79356998,-#_e97dcfb1b68795538757ef2464230176p8@RASGRF1
4.18e-87FFCP PHASE2:Hg19::chr2:25720324..25720333,-#_6f05ef33c9ee70d3660616c020973ea8p15@DTNB
4.18e-87FFCP PHASE1:Hg19::chr2:25720324..25720333,-#_6f05ef33c9ee70d3660616c020973ea8p15@DTNB
4.42e-84FFCP PHASE2:Hg19::chr12:26765770..26765792,-#_6d8e8da43032288fecb6bd22e7fe7651p@chr12:26765770..26765792, -
4.42e-84FFCP PHASE1:Hg19::chr12:26765770..26765792,-#_6d8e8da43032288fecb6bd22e7fe7651p@chr12:26765770..26765792, -
5.98e-82FFCP PHASE2:Hg19::chr14:62010202..62010207,-#_504247f84064adbd5cf0c54ed2baa110p@chr14:62010202..62010207, -
5.98e-82FFCP PHASE1:Hg19::chr14:62010202..62010207,-#_504247f84064adbd5cf0c54ed2baa110p@chr14:62010202..62010207, -
1.38e-81FFCP PHASE1:Hg19::chr2:179739649..179739660,-#_8c23122acc4efb7cbcd934ecb6e3af80p@chr2:179739649..179739660, -
1.38e-81FFCP PHASE2:Hg19::chr2:179739649..179739660,-#_8c23122acc4efb7cbcd934ecb6e3af80p@chr2:179739649..179739660, -
2.71e-79FFCP PHASE1:Hg19::chr5:151304948..151304984,-#_c1f753ce80d9148ee5880ebd57b17b4dp@chr5:151304948..151304984, -
2.71e-79FFCP PHASE2:Hg19::chr5:151304948..151304984,-#_c1f753ce80d9148ee5880ebd57b17b4dp@chr5:151304948..151304984, -
4.66e-79FFCP PHASE1:Hg19::chr4:79892974..79892983,+#_7c295724bc1a2dea737d9ee4d73aca55p8@LOC100505875
4.66e-79FFCP PHASE2:Hg19::chr4:79892974..79892983,+#_7c295724bc1a2dea737d9ee4d73aca55p8@LOC100505875
1.56e-78FFCP PHASE2:Hg19::chr18:74754861..74754870,+#_3c0d204eae8bb047f555d5fc42a2d6e7p@chr18:74754861..74754870, +
1.56e-78FFCP PHASE1:Hg19::chr18:74754861..74754870,+#_3c0d204eae8bb047f555d5fc42a2d6e7p@chr18:74754861..74754870, +
4.57e-78FFCP PHASE2:Hg19::chrX:145936111..145936120,+#_154075bf1804a5d8f464c29c75822c21p@chrX:145936111..145936120, +
4.57e-78FFCP PHASE1:Hg19::chrX:145936111..145936120,+#_154075bf1804a5d8f464c29c75822c21p@chrX:145936111..145936120, +
1.98e-77FFCP PHASE2:Hg19::chr14:105833371..105833383,+#_5897743b91f7f9d4925a4b9b131059dbp@chr14:105833371..105833383, +
1.98e-77FFCP PHASE1:Hg19::chr14:105833371..105833383,+#_5897743b91f7f9d4925a4b9b131059dbp@chr14:105833371..105833383, +
2.17e-75FFCP PHASE1:Hg19::chr5:151304987..151304998,-#_d080f732a55f5218d6bf96d995e7854dp@chr5:151304987..151304998, -
2.17e-75FFCP PHASE2:Hg19::chr5:151304987..151304998,-#_d080f732a55f5218d6bf96d995e7854dp@chr5:151304987..151304998, -
3.86e-75FFCP PHASE2:Hg19::chr2:234077664..234077672,+#_d61d5e5782fbd629850d1487ef2db2bep@chr2:234077664..234077672, +
3.86e-75FFCP PHASE1:Hg19::chr2:234077664..234077672,+#_d61d5e5782fbd629850d1487ef2db2bep@chr2:234077664..234077672, +
3.86e-75FFCP PHASE1:Hg19::chr5:150050170..150050182,+#_d61d5e5782fbd629850d1487ef2db2bep@chr5:150050170..150050182, +
3.86e-75FFCP PHASE2:Hg19::chr5:150050170..150050182,+#_d61d5e5782fbd629850d1487ef2db2bep@chr5:150050170..150050182, +
6.85e-75FFCP PHASE1:Hg19::chr11:30751827..30751838,+#_b24dabdffb401a06927acd2179048f55p@chr11:30751827..30751838, +
6.85e-75FFCP PHASE2:Hg19::chr11:30751827..30751838,+#_b24dabdffb401a06927acd2179048f55p@chr11:30751827..30751838, +
8.29e-75FFCP PHASE2:Hg19::chr1:155940355..155940366,-#_68f3f184de75f74ffe779ecfdec9e252p43@ARHGEF2
8.29e-75FFCP PHASE2:Hg19::chr15:79356834..79356842,-#_68f3f184de75f74ffe779ecfdec9e252p15@RASGRF1
8.29e-75FFCP PHASE1:Hg19::chr1:155940355..155940366,-#_68f3f184de75f74ffe779ecfdec9e252p43@ARHGEF2
8.29e-75FFCP PHASE1:Hg19::chr15:79356834..79356842,-#_68f3f184de75f74ffe779ecfdec9e252p15@RASGRF1
1.11e-74FFCP PHASE1:Hg19::chr14:91932629..91932652,-#_a8fc99f7f43a516ecea4dae34ea0cf20p14@SMEK1
1.11e-74FFCP PHASE2:Hg19::chr14:91932629..91932652,-#_a8fc99f7f43a516ecea4dae34ea0cf20p14@SMEK1
1.21e-74FFCP PHASE2:Hg19::chr17:65489258..65489261,-#_c403b3db3e18742fc3fdd35bf6599a6ep@chr17:65489258..65489261, -
1.21e-74FFCP PHASE1:Hg19::chr17:65489258..65489261,-#_c403b3db3e18742fc3fdd35bf6599a6ep@chr17:65489258..65489261, -
1.51e-74FFCP PHASE2:Hg19::chr17:42984370..42984375,-#_217d93db50b7a0ada83dc3a51d7c0406p42@GFAP
1.51e-74FFCP PHASE1:Hg19::chr15:91447008..91447017,+#_217d93db50b7a0ada83dc3a51d7c0406p25@MAN2A2
1.51e-74FFCP PHASE1:Hg19::chr17:42984370..42984375,-#_217d93db50b7a0ada83dc3a51d7c0406p42@GFAP
1.51e-74FFCP PHASE2:Hg19::chr15:91447008..91447017,+#_217d93db50b7a0ada83dc3a51d7c0406p25@MAN2A2
2.46e-74FFCP PHASE2:Hg19::chr7:147336227..147336236,+#_25438a5d0302e3b9b4dcef49493c3cbdp18@CNTNAP2
2.46e-74FFCP PHASE1:Hg19::chr7:147336227..147336236,+#_25438a5d0302e3b9b4dcef49493c3cbdp18@CNTNAP2
5.92e-74FFCP PHASE1:Hg19::chr14:105833352..105833361,+#_9f1a4f9dca51c66c5ebbb24de5941e20p@chr14:105833352..105833361, +
5.92e-74FFCP PHASE2:Hg19::chr14:105833352..105833361,+#_9f1a4f9dca51c66c5ebbb24de5941e20p@chr14:105833352..105833361, +
8.7e-74FFCP PHASE2:Hg19::chr5:77302570..77302586,+#_e3c630d4f2b9cb7764a72255ae43f5e7p@chr5:77302570..77302586, +
8.7e-74FFCP PHASE1:Hg19::chr5:77302570..77302586,+#_e3c630d4f2b9cb7764a72255ae43f5e7p@chr5:77302570..77302586, +
2.1e-73FFCP PHASE2:Hg19::chrX:106692537..106692551,+#_75cf0a4b97ef2d68fceb1026debbcf7cp@chrX:106692537..106692551, +
2.1e-73FFCP PHASE1:Hg19::chrX:106692537..106692551,+#_75cf0a4b97ef2d68fceb1026debbcf7cp@chrX:106692537..106692551, +
2.54e-70FFCP PHASE1:Hg19::chr2:25720404..25720435,-#_c119923ef128471785e1860e4c08d5bap8@DTNB
2.54e-70FFCP PHASE2:Hg19::chr2:25720404..25720435,-#_c119923ef128471785e1860e4c08d5bap8@DTNB
1.34e-69FFCP PHASE2:Hg19::chr15:79356860..79356874,-#_597b963268f97c661473ff8ad87d039ap9@RASGRF1
1.34e-69FFCP PHASE1:Hg19::chr15:79356860..79356874,-#_597b963268f97c661473ff8ad87d039ap9@RASGRF1
3.9e-69FFCP PHASE2:Hg19::chr5:152082403..152082408,+#_85d94ec934dab7823c474efef1b62692p@chr5:152082403..152082408, +
3.9e-69FFCP PHASE1:Hg19::chr5:152082403..152082408,+#_85d94ec934dab7823c474efef1b62692p@chr5:152082403..152082408, +
6.26e-69FFCP PHASE2:Hg19::chr21:18811205..18811216,+#_a72d345ba2e4217f16055127d73c6ab7p3@C21orf37
6.26e-69FFCP PHASE1:Hg19::chr21:18811205..18811216,+#_a72d345ba2e4217f16055127d73c6ab7p3@C21orf37
7.27e-69FFCP PHASE2:Hg19::chr4:34621389..34621413,+#_9cd6c582a9ff8384404c33cfdcbab05cp@chr4:34621389..34621413, +
7.27e-69FFCP PHASE1:Hg19::chr4:34621389..34621413,+#_9cd6c582a9ff8384404c33cfdcbab05cp@chr4:34621389..34621413, +
1.46e-68FFCP PHASE1:Hg19::chrX:16753203..16753238,+#_aa3378aac3944bb422a3da8fd63a1204p@chrX:16753203..16753238, +
1.46e-68FFCP PHASE2:Hg19::chrX:16753203..16753238,+#_aa3378aac3944bb422a3da8fd63a1204p@chrX:16753203..16753238, +
1.47e-66FFCP PHASE1:Hg19::chr15:93616900..93616918,-#_15d312fbf39ad5233a3208aade390686p6@RGMA
1.47e-66FFCP PHASE2:Hg19::chr15:93616900..93616918,-#_15d312fbf39ad5233a3208aade390686p6@RGMA
1.87e-66FFCP PHASE2:Hg19::chr18:5577640..5577652,-#_43eddf22ed52394d9aaed4c2c7fd540dp14@EPB41L3
1.87e-66FFCP PHASE1:Hg19::chr18:5577640..5577652,-#_43eddf22ed52394d9aaed4c2c7fd540dp14@EPB41L3
2.06e-66FFCP PHASE1:Hg19::chr2:25720352..25720388,-#_e880f46bf4e87ab966374e9c57c59655p7@DTNB
2.06e-66FFCP PHASE2:Hg19::chr2:25720352..25720388,-#_e880f46bf4e87ab966374e9c57c59655p7@DTNB
2.83e-66FFCP PHASE2:Hg19::chr6:132580699..132580702,+#_2a2041befc4eada1b7dd8cbc01329371p@chr6:132580699..132580702, +
2.83e-66FFCP PHASE1:Hg19::chr6:132580699..132580702,+#_2a2041befc4eada1b7dd8cbc01329371p@chr6:132580699..132580702, +
2.83e-66FFCP PHASE1:Hg19::chr11:3224990..3225000,-#_2a2041befc4eada1b7dd8cbc01329371p@chr11:3224990..3225000, -
2.83e-66FFCP PHASE2:Hg19::chr5:35090057..35090065,-#_2a2041befc4eada1b7dd8cbc01329371p27@PRLR
2.83e-66FFCP PHASE2:Hg19::chr4:117675642..117675654,+#_2a2041befc4eada1b7dd8cbc01329371p@chr4:117675642..117675654, +
2.83e-66FFCP PHASE1:Hg19::chr6:56820018..56820029,+#_2a2041befc4eada1b7dd8cbc01329371p16@BEND6
2.83e-66FFCP PHASE2:Hg19::chr12:33592574..33592584,-#_2a2041befc4eada1b7dd8cbc01329371p6@SYT10
2.83e-66FFCP PHASE1:Hg19::chr5:35090057..35090065,-#_2a2041befc4eada1b7dd8cbc01329371p27@PRLR
2.83e-66FFCP PHASE2:Hg19::chr2:237146889..237146895,-#_2a2041befc4eada1b7dd8cbc01329371p@chr2:237146889..237146895, -
2.83e-66FFCP PHASE1:Hg19::chr2:237146889..237146895,-#_2a2041befc4eada1b7dd8cbc01329371p@chr2:237146889..237146895, -
2.83e-66FFCP PHASE1:Hg19::chr5:35090318..35090324,-#_2a2041befc4eada1b7dd8cbc01329371p@chr5:35090318..35090324, -
2.83e-66FFCP PHASE1:Hg19::chr12:33592574..33592584,-#_2a2041befc4eada1b7dd8cbc01329371p6@SYT10
2.83e-66FFCP PHASE2:Hg19::chr6:56820018..56820029,+#_2a2041befc4eada1b7dd8cbc01329371p16@BEND6
2.83e-66FFCP PHASE1:Hg19::chr12:44467410..44467418,+#_2a2041befc4eada1b7dd8cbc01329371p13@TMEM117










Property "Property value" (as page type) with input value "UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" xsd:string" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.

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