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|name=brainstem
|name=brainstem
|namespace=
|namespace=
|def="The brainstem (or brain stem) is the lower part of the brain, adjoining and structurally continuous with the spinal cord. The brain stem provides the main motor and sensory innervation to the face and neck via the cranial nerves. Though small, this is an extremely important part of the brain as the nerve connections of the motor and sensory systems from the main part of the brain to the rest of the body pass through the brain stem. This includes the corticospinal tract (motor), the posterior column-medial lemniscus pathway (fine touch, vibration sensation and proprioception) and the spinothalamic tract (pain, temperature, itch and crude touch). The brain stem also plays an important role in the regulation of cardiac and respiratory function. It also regulates the central nervous system, and is pivotal in maintaining consciousness and regulating the sleep cycle. Some taxonomies describe the brain stem as the medulla oblongata (myelencephalon) and pons (part of metencephalon), whereas others include the midbrain (mesencephalon). [WP,unvetted]." [Wikipedia:Brainstem]
|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/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;;VHOG:0001457;;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
|is_a=UBERON:0002616;;UBERON:0010314
|synonym="brain stem" EXACT [ABA:BS];;"truncus encephalicus" RELATED [BTO:0000146]
|synonym="brain stem" EXACT [ABA:BS];;"truncus encephali" EXACT LATIN [Wikipedia:Brainstem];;"truncus encephalicus" RELATED [BTO:0000146]
|comment=ZFA includes the tegmentum, MA the whole midbrain. Both include medulla oblongata. Here we make an overlaps link between midbrain and brainstem. Note that ABA states that cerebellum and brainstem are spatially disjoint. We do NOT include this axiom here, as it leads to multiple inconsistencies. This needs addressed in more detail.
|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
|alt_id=UBERON:FMA_79876-MA_0000169
|disjoint_from=
|disjoint_from=
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|created_by=
|created_by=
|obo_creation_date=
|obo_creation_date=
|subset=uberon_slim;;vertebrate_core
|subset=loose_concept;;uberon_slim;;vertebrate_core
|adjacent_to=
|derives_from=
|derives_from=
|develops_from=
|develops_from=
|has_quality=
|has_quality=
|located_in=
|located_in=
|part_of=UBERON:0000955
|part_of=
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|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=
|is_obsolete=
|preceded_by=
|preceded_by=
}}
}}

Revision as of 17:01, 26 June 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)



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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