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UBERON:0002298

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Name:brainstem
Namespace:FANTOM
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
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: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
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
Analyst: Hideya Kawaji

link to source dataset
human : data
mouse : data

P-valueFFCPShort description
1.73e-118FFCP PHASE1:Hg19::chr12:72332618..72332632,+#_d66ad30c28141a4c845f221a2986ef7dp1@TPH2
1.73e-118FFCP PHASE2:Hg19::chr12:72332618..72332632,+#_d66ad30c28141a4c845f221a2986ef7dp1@TPH2
8.05e-117FFCP PHASE1:Hg19::chr4:117675601..117675614,+#_26af8d56ec17fc966bdd14c58c12aad5p@chr4:117675601..117675614, +
8.05e-117FFCP PHASE2: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 PHASE1:Hg19::chr2:72381655..72381673,-#_bea5de2b5ee97e65a786fdea7453c81ep@chr2:72381655..72381673, -
1.57e-98FFCP PHASE2:Hg19::chr2:72381655..72381673,-#_bea5de2b5ee97e65a786fdea7453c81ep@chr2:72381655..72381673, -
1.83e-98FFCP PHASE1:Hg19::chr16:49670005..49670020,-#_c04181094e2512171daa4dd2b2cfbb3cp@chr16:49670005..49670020, -
1.83e-98FFCP PHASE2:Hg19::chr16:49670005..49670020,-#_c04181094e2512171daa4dd2b2cfbb3cp@chr16:49670005..49670020, -
1.83e-98FFCP PHASE2:Hg19::chr5:126959224..126959239,+#_c04181094e2512171daa4dd2b2cfbb3cp@chr5:126959224..126959239, +
1.83e-98FFCP PHASE1:Hg19::chr5:126959224..126959239,+#_c04181094e2512171daa4dd2b2cfbb3cp@chr5:126959224..126959239, +
3.65e-98FFCP PHASE1:Hg19::chr16:290098..290109,+#_813d16cf0267b3f104241a123c3f51d6p13@ITFG3
3.65e-98FFCP PHASE2:Hg19::chr16:290098..290109,+#_813d16cf0267b3f104241a123c3f51d6p13@ITFG3
3.09e-91FFCP PHASE2:Hg19::chr15:60296481..60296492,+#_8178043de3e7d98d976ba929467e07d8p7@FOXB1
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
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 PHASE1:Hg19::chr12:26765770..26765792,-#_6d8e8da43032288fecb6bd22e7fe7651p@chr12:26765770..26765792, -
4.42e-84FFCP PHASE2: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 PHASE2:Hg19::chr2:179739649..179739660,-#_8c23122acc4efb7cbcd934ecb6e3af80p@chr2:179739649..179739660, -
1.38e-81FFCP PHASE1: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 PHASE2:Hg19::chr4:79892974..79892983,+#_7c295724bc1a2dea737d9ee4d73aca55p8@LOC100505875
4.66e-79FFCP PHASE1: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 PHASE1:Hg19::chrX:145936111..145936120,+#_154075bf1804a5d8f464c29c75822c21p@chrX:145936111..145936120, +
4.57e-78FFCP PHASE2: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::chr5:150050170..150050182,+#_d61d5e5782fbd629850d1487ef2db2bep@chr5:150050170..150050182, +
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, +
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 PHASE1:Hg19::chr15:79356834..79356842,-#_68f3f184de75f74ffe779ecfdec9e252p15@RASGRF1
8.29e-75FFCP PHASE1:Hg19::chr1:155940355..155940366,-#_68f3f184de75f74ffe779ecfdec9e252p43@ARHGEF2
8.29e-75FFCP PHASE2:Hg19::chr1:155940355..155940366,-#_68f3f184de75f74ffe779ecfdec9e252p43@ARHGEF2
8.29e-75FFCP PHASE2:Hg19::chr15:79356834..79356842,-#_68f3f184de75f74ffe779ecfdec9e252p15@RASGRF1
1.11e-74FFCP PHASE2:Hg19::chr14:91932629..91932652,-#_a8fc99f7f43a516ecea4dae34ea0cf20p14@SMEK1
1.11e-74FFCP PHASE1:Hg19::chr14:91932629..91932652,-#_a8fc99f7f43a516ecea4dae34ea0cf20p14@SMEK1
1.21e-74FFCP PHASE1:Hg19::chr17:65489258..65489261,-#_c403b3db3e18742fc3fdd35bf6599a6ep@chr17:65489258..65489261, -
1.21e-74FFCP PHASE2:Hg19::chr17:65489258..65489261,-#_c403b3db3e18742fc3fdd35bf6599a6ep@chr17:65489258..65489261, -
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
1.51e-74FFCP PHASE2:Hg19::chr17:42984370..42984375,-#_217d93db50b7a0ada83dc3a51d7c0406p42@GFAP
2.46e-74FFCP PHASE1:Hg19::chr7:147336227..147336236,+#_25438a5d0302e3b9b4dcef49493c3cbdp18@CNTNAP2
2.46e-74FFCP PHASE2: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 PHASE1:Hg19::chr5:77302570..77302586,+#_e3c630d4f2b9cb7764a72255ae43f5e7p@chr5:77302570..77302586, +
8.7e-74FFCP PHASE2: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 PHASE2:Hg19::chr2:25720404..25720435,-#_c119923ef128471785e1860e4c08d5bap8@DTNB
2.54e-70FFCP PHASE1: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 PHASE1:Hg19::chr21:18811205..18811216,+#_a72d345ba2e4217f16055127d73c6ab7p3@C21orf37
6.26e-69FFCP PHASE2:Hg19::chr21:18811205..18811216,+#_a72d345ba2e4217f16055127d73c6ab7p3@C21orf37
7.27e-69FFCP PHASE1:Hg19::chr4:34621389..34621413,+#_9cd6c582a9ff8384404c33cfdcbab05cp@chr4:34621389..34621413, +
7.27e-69FFCP PHASE2: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,+#_aa3378aac3944bb422a3da8fd63a1204+, p@chrX:16753203..16753238
1.47e-66FFCP PHASE2:Hg19::chr15:93616900..93616918,-#_15d312fbf39ad5233a3208aade390686p6@RGMA
1.47e-66FFCP PHASE1:Hg19::chr15:93616900..93616918,-#_15d312fbf39ad5233a3208aade390686p6@RGMA
1.87e-66FFCP PHASE1:Hg19::chr18:5577640..5577652,-#_43eddf22ed52394d9aaed4c2c7fd540dp14@EPB41L3
1.87e-66FFCP PHASE2: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::chr12:33592574..33592584,-#_2a2041befc4eada1b7dd8cbc01329371p6@SYT10
2.83e-66FFCP PHASE2:Hg19::chr12:44467410..44467418,+#_2a2041befc4eada1b7dd8cbc01329371p13@TMEM117
2.83e-66FFCP PHASE2:Hg19::chr2:218873244..218873256,-#_2a2041befc4eada1b7dd8cbc01329371p@chr2:218873244..218873256, -
2.83e-66FFCP PHASE2:Hg19::chr2:237146889..237146895,-#_2a2041befc4eada1b7dd8cbc01329371p@chr2:237146889..237146895, -
2.83e-66FFCP PHASE2:Hg19::chr2:8851401..8851408,+#_2a2041befc4eada1b7dd8cbc01329371p@chr2:8851401..8851408, +
2.83e-66FFCP PHASE1:Hg19::chr4:117675642..117675654,+#_2a2041befc4eada1b7dd8cbc01329371p@chr4:117675642..117675654, +
2.83e-66FFCP PHASE1:Hg19::chr5:35090057..35090065,-#_2a2041befc4eada1b7dd8cbc01329371p27@PRLR
2.83e-66FFCP PHASE1:Hg19::chr5:35090318..35090324,-#_2a2041befc4eada1b7dd8cbc01329371p@chr5:35090318..35090324, -
2.83e-66FFCP PHASE1:Hg19::chr6:132580699..132580702,+#_2a2041befc4eada1b7dd8cbc01329371p@chr6:132580699..132580702, +
2.83e-66FFCP PHASE1:Hg19::chr6:56820018..56820029,+#_2a2041befc4eada1b7dd8cbc01329371p16@BEND6
2.83e-66FFCP PHASE2:Hg19::chr11:3224990..3225000,-#_2a2041befc4eada1b7dd8cbc01329371p@chr11:3224990..3225000, -
2.83e-66FFCP PHASE2:Hg19::chr6:56820018..56820029,+#_2a2041befc4eada1b7dd8cbc01329371p16@BEND6
2.83e-66FFCP PHASE2:Hg19::chr4:117675642..117675654,+#_2a2041befc4eada1b7dd8cbc01329371p@chr4:117675642..117675654, +
2.83e-66FFCP PHASE1:Hg19::chr2:218873244..218873256,-#_2a2041befc4eada1b7dd8cbc01329371p@chr2:218873244..218873256, -










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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