UBERON:0002298: Difference between revisions
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|part_of= | |part_of=UBERON:0000955 | ||
|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= | |is_obsolete= | ||
|preceded_by= | |preceded_by= | ||
}} | }} | ||
Revision as of 13:31, 27 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: |
| ||
| 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 |
Gray719.png]
200px-Gray719.png]
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)
- 10033-101E6 (pons, adult, pool1)
- 10038-101F2 (medulla oblongata, adult, pool1)
- 10155-103A2 (medulla oblongata, adult, donor10252)
- 10165-103B3 (locus coeruleus, adult, donor10252)
- 10174-103C3 (medulla oblongata - adult, donor10196)
- 10182-103D2 (locus coeruleus - adult, donor10196)
- 10361-105F1 (medulla oblongata, newborn, donor10223)
- 10362-105F2 (locus coeruleus, newborn, donor10223)
- 10375-105G6 (locus coeruleus, adult, donor10258)
- 1396-42A3 (medulla oblongata, neonate N30)
... further results Mouse (Mus musculus)
- 10033-101E6 (pons, adult, pool1)
- 10038-101F2 (medulla oblongata, adult, pool1)
- 10155-103A2 (medulla oblongata, adult, donor10252)
- 10165-103B3 (locus coeruleus, adult, donor10252)
- 10174-103C3 (medulla oblongata - adult, donor10196)
- 10182-103D2 (locus coeruleus - adult, donor10196)
- 10361-105F1 (medulla oblongata, newborn, donor10223)
- 10362-105F2 (locus coeruleus, newborn, donor10223)
- 10375-105G6 (locus coeruleus, adult, donor10258)
- 1396-42A3 (medulla oblongata, neonate N30)
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-value | FFCP | Short description |
|---|---|---|
| 1.73e-118 | FFCP PHASE2:Hg19::chr12:72332618..72332632,+#_d66ad30c28141a4c845f221a2986ef7d | p1@TPH2 |
| 1.73e-118 | FFCP PHASE1:Hg19::chr12:72332618..72332632,+#_d66ad30c28141a4c845f221a2986ef7d | p1@TPH2 |
| 8.05e-117 | FFCP PHASE2:Hg19::chr4:117675601..117675614,+#_26af8d56ec17fc966bdd14c58c12aad5 | p@chr4:117675601..117675614, + |
| 8.05e-117 | FFCP PHASE1:Hg19::chr4:117675601..117675614,+#_26af8d56ec17fc966bdd14c58c12aad5 | p@chr4:117675601..117675614, + |
| 1.65e-116 | FFCP PHASE2:Hg19::chr2:69741832..69741847,-#_1ce75deb9f06e2af9d3128d156b22e91 | p@chr2:69741832..69741847, - |
| 1.65e-116 | FFCP PHASE1:Hg19::chr2:69741832..69741847,-#_1ce75deb9f06e2af9d3128d156b22e91 | p@chr2:69741832..69741847, - |
| 5.07e-102 | FFCP PHASE2:Hg19::chr9:128998376..128998387,-#_8f494f2b182dd0c1aae0f2bae2018a44 | p@chr9:128998376..128998387, - |
| 5.07e-102 | FFCP PHASE1:Hg19::chr9:128998376..128998387,-#_8f494f2b182dd0c1aae0f2bae2018a44 | p@chr9:128998376..128998387, - |
| 1.57e-98 | FFCP PHASE2:Hg19::chr2:72381655..72381673,-#_bea5de2b5ee97e65a786fdea7453c81e | p@chr2:72381655..72381673, - |
| 1.57e-98 | FFCP PHASE1:Hg19::chr2:72381655..72381673,-#_bea5de2b5ee97e65a786fdea7453c81e | p@chr2:72381655..72381673, - |
| 1.83e-98 | FFCP PHASE1:Hg19::chr5:126959224..126959239,+#_c04181094e2512171daa4dd2b2cfbb3c | p@chr5:126959224..126959239, + |
| 1.83e-98 | FFCP PHASE1:Hg19::chr16:49670005..49670020,-#_c04181094e2512171daa4dd2b2cfbb3c | p@chr16:49670005..49670020, - |
| 1.83e-98 | FFCP PHASE2:Hg19::chr5:126959224..126959239,+#_c04181094e2512171daa4dd2b2cfbb3c | p@chr5:126959224..126959239, + |
| 1.83e-98 | FFCP PHASE2:Hg19::chr16:49670005..49670020,-#_c04181094e2512171daa4dd2b2cfbb3c | p@chr16:49670005..49670020, - |
| 3.65e-98 | FFCP PHASE2:Hg19::chr16:290098..290109,+#_813d16cf0267b3f104241a123c3f51d6 | p13@ITFG3 |
| 3.65e-98 | FFCP PHASE1:Hg19::chr16:290098..290109,+#_813d16cf0267b3f104241a123c3f51d6 | p13@ITFG3 |
| 3.09e-91 | FFCP PHASE1:Hg19::chr11:20621148..20621166,+#_8178043de3e7d98d976ba929467e07d8 | p1@SLC6A5 |
| 3.09e-91 | FFCP PHASE2:Hg19::chr11:20621148..20621166,+#_8178043de3e7d98d976ba929467e07d8 | p1@SLC6A5 |
| 3.09e-91 | FFCP PHASE1:Hg19::chr15:60296481..60296492,+#_8178043de3e7d98d976ba929467e07d8 | p7@FOXB1 |
| 3.09e-91 | FFCP PHASE2:Hg19::chr15:60296481..60296492,+#_8178043de3e7d98d976ba929467e07d8 | p7@FOXB1 |
| 8.11e-91 | FFCP PHASE1:Hg19::chr15:79356984..79356998,-#_e97dcfb1b68795538757ef2464230176 | p8@RASGRF1 |
| 8.11e-91 | FFCP PHASE2:Hg19::chr15:79356984..79356998,-#_e97dcfb1b68795538757ef2464230176 | p8@RASGRF1 |
| 4.18e-87 | FFCP PHASE2:Hg19::chr2:25720324..25720333,-#_6f05ef33c9ee70d3660616c020973ea8 | p15@DTNB |
| 4.18e-87 | FFCP PHASE1:Hg19::chr2:25720324..25720333,-#_6f05ef33c9ee70d3660616c020973ea8 | p15@DTNB |
| 4.42e-84 | FFCP PHASE2:Hg19::chr12:26765770..26765792,-#_6d8e8da43032288fecb6bd22e7fe7651 | p@chr12:26765770..26765792, - |
| 4.42e-84 | FFCP PHASE1:Hg19::chr12:26765770..26765792,-#_6d8e8da43032288fecb6bd22e7fe7651 | p@chr12:26765770..26765792, - |
| 5.98e-82 | FFCP PHASE2:Hg19::chr14:62010202..62010207,-#_504247f84064adbd5cf0c54ed2baa110 | p@chr14:62010202..62010207, - |
| 5.98e-82 | FFCP PHASE1:Hg19::chr14:62010202..62010207,-#_504247f84064adbd5cf0c54ed2baa110 | p@chr14:62010202..62010207, - |
| 1.38e-81 | FFCP PHASE1:Hg19::chr2:179739649..179739660,-#_8c23122acc4efb7cbcd934ecb6e3af80 | p@chr2:179739649..179739660, - |
| 1.38e-81 | FFCP PHASE2:Hg19::chr2:179739649..179739660,-#_8c23122acc4efb7cbcd934ecb6e3af80 | p@chr2:179739649..179739660, - |
| 2.71e-79 | FFCP PHASE1:Hg19::chr5:151304948..151304984,-#_c1f753ce80d9148ee5880ebd57b17b4d | p@chr5:151304948..151304984, - |
| 2.71e-79 | FFCP PHASE2:Hg19::chr5:151304948..151304984,-#_c1f753ce80d9148ee5880ebd57b17b4d | p@chr5:151304948..151304984, - |
| 4.66e-79 | FFCP PHASE1:Hg19::chr4:79892974..79892983,+#_7c295724bc1a2dea737d9ee4d73aca55 | p8@LOC100505875 |
| 4.66e-79 | FFCP PHASE2:Hg19::chr4:79892974..79892983,+#_7c295724bc1a2dea737d9ee4d73aca55 | p8@LOC100505875 |
| 1.56e-78 | FFCP PHASE2:Hg19::chr18:74754861..74754870,+#_3c0d204eae8bb047f555d5fc42a2d6e7 | p@chr18:74754861..74754870, + |
| 1.56e-78 | FFCP PHASE1:Hg19::chr18:74754861..74754870,+#_3c0d204eae8bb047f555d5fc42a2d6e7 | p@chr18:74754861..74754870, + |
| 4.57e-78 | FFCP PHASE2:Hg19::chrX:145936111..145936120,+#_154075bf1804a5d8f464c29c75822c21 | p@chrX:145936111..145936120, + |
| 4.57e-78 | FFCP PHASE1:Hg19::chrX:145936111..145936120,+#_154075bf1804a5d8f464c29c75822c21 | p@chrX:145936111..145936120, + |
| 1.98e-77 | FFCP PHASE2:Hg19::chr14:105833371..105833383,+#_5897743b91f7f9d4925a4b9b131059db | p@chr14:105833371..105833383, + |
| 1.98e-77 | FFCP PHASE1:Hg19::chr14:105833371..105833383,+#_5897743b91f7f9d4925a4b9b131059db | p@chr14:105833371..105833383, + |
| 2.17e-75 | FFCP PHASE1:Hg19::chr5:151304987..151304998,-#_d080f732a55f5218d6bf96d995e7854d | p@chr5:151304987..151304998, - |
| 2.17e-75 | FFCP PHASE2:Hg19::chr5:151304987..151304998,-#_d080f732a55f5218d6bf96d995e7854d | p@chr5:151304987..151304998, - |
| 3.86e-75 | FFCP PHASE2:Hg19::chr2:234077664..234077672,+#_d61d5e5782fbd629850d1487ef2db2be | p@chr2:234077664..234077672, + |
| 3.86e-75 | FFCP PHASE1:Hg19::chr2:234077664..234077672,+#_d61d5e5782fbd629850d1487ef2db2be | p@chr2:234077664..234077672, + |
| 3.86e-75 | FFCP PHASE1:Hg19::chr5:150050170..150050182,+#_d61d5e5782fbd629850d1487ef2db2be | p@chr5:150050170..150050182, + |
| 3.86e-75 | FFCP PHASE2:Hg19::chr5:150050170..150050182,+#_d61d5e5782fbd629850d1487ef2db2be | p@chr5:150050170..150050182, + |
| 6.85e-75 | FFCP PHASE1:Hg19::chr11:30751827..30751838,+#_b24dabdffb401a06927acd2179048f55 | p@chr11:30751827..30751838, + |
| 6.85e-75 | FFCP PHASE2:Hg19::chr11:30751827..30751838,+#_b24dabdffb401a06927acd2179048f55 | p@chr11:30751827..30751838, + |
| 8.29e-75 | FFCP PHASE2:Hg19::chr1:155940355..155940366,-#_68f3f184de75f74ffe779ecfdec9e252 | p43@ARHGEF2 |
| 8.29e-75 | FFCP PHASE2:Hg19::chr15:79356834..79356842,-#_68f3f184de75f74ffe779ecfdec9e252 | p15@RASGRF1 |
| 8.29e-75 | FFCP PHASE1:Hg19::chr1:155940355..155940366,-#_68f3f184de75f74ffe779ecfdec9e252 | p43@ARHGEF2 |
| 8.29e-75 | FFCP PHASE1:Hg19::chr15:79356834..79356842,-#_68f3f184de75f74ffe779ecfdec9e252 | p15@RASGRF1 |
| 1.11e-74 | FFCP PHASE1:Hg19::chr14:91932629..91932652,-#_a8fc99f7f43a516ecea4dae34ea0cf20 | p14@SMEK1 |
| 1.11e-74 | FFCP PHASE2:Hg19::chr14:91932629..91932652,-#_a8fc99f7f43a516ecea4dae34ea0cf20 | p14@SMEK1 |
| 1.21e-74 | FFCP PHASE2:Hg19::chr17:65489258..65489261,-#_c403b3db3e18742fc3fdd35bf6599a6e | p@chr17:65489258..65489261, - |
| 1.21e-74 | FFCP PHASE1:Hg19::chr17:65489258..65489261,-#_c403b3db3e18742fc3fdd35bf6599a6e | p@chr17:65489258..65489261, - |
| 1.51e-74 | FFCP PHASE2:Hg19::chr17:42984370..42984375,-#_217d93db50b7a0ada83dc3a51d7c0406 | p42@GFAP |
| 1.51e-74 | FFCP PHASE1:Hg19::chr15:91447008..91447017,+#_217d93db50b7a0ada83dc3a51d7c0406 | p25@MAN2A2 |
| 1.51e-74 | FFCP PHASE1:Hg19::chr17:42984370..42984375,-#_217d93db50b7a0ada83dc3a51d7c0406 | p42@GFAP |
| 1.51e-74 | FFCP PHASE2:Hg19::chr15:91447008..91447017,+#_217d93db50b7a0ada83dc3a51d7c0406 | p25@MAN2A2 |
| 2.46e-74 | FFCP PHASE2:Hg19::chr7:147336227..147336236,+#_25438a5d0302e3b9b4dcef49493c3cbd | p18@CNTNAP2 |
| 2.46e-74 | FFCP PHASE1:Hg19::chr7:147336227..147336236,+#_25438a5d0302e3b9b4dcef49493c3cbd | p18@CNTNAP2 |
| 5.92e-74 | FFCP PHASE1:Hg19::chr14:105833352..105833361,+#_9f1a4f9dca51c66c5ebbb24de5941e20 | p@chr14:105833352..105833361, + |
| 5.92e-74 | FFCP PHASE2:Hg19::chr14:105833352..105833361,+#_9f1a4f9dca51c66c5ebbb24de5941e20 | p@chr14:105833352..105833361, + |
| 8.7e-74 | FFCP PHASE2:Hg19::chr5:77302570..77302586,+#_e3c630d4f2b9cb7764a72255ae43f5e7 | p@chr5:77302570..77302586, + |
| 8.7e-74 | FFCP PHASE1:Hg19::chr5:77302570..77302586,+#_e3c630d4f2b9cb7764a72255ae43f5e7 | p@chr5:77302570..77302586, + |
| 2.1e-73 | FFCP PHASE2:Hg19::chrX:106692537..106692551,+#_75cf0a4b97ef2d68fceb1026debbcf7c | p@chrX:106692537..106692551, + |
| 2.1e-73 | FFCP PHASE1:Hg19::chrX:106692537..106692551,+#_75cf0a4b97ef2d68fceb1026debbcf7c | p@chrX:106692537..106692551, + |
| 2.54e-70 | FFCP PHASE1:Hg19::chr2:25720404..25720435,-#_c119923ef128471785e1860e4c08d5ba | p8@DTNB |
| 2.54e-70 | FFCP PHASE2:Hg19::chr2:25720404..25720435,-#_c119923ef128471785e1860e4c08d5ba | p8@DTNB |
| 1.34e-69 | FFCP PHASE2:Hg19::chr15:79356860..79356874,-#_597b963268f97c661473ff8ad87d039a | p9@RASGRF1 |
| 1.34e-69 | FFCP PHASE1:Hg19::chr15:79356860..79356874,-#_597b963268f97c661473ff8ad87d039a | p9@RASGRF1 |
| 3.9e-69 | FFCP PHASE2:Hg19::chr5:152082403..152082408,+#_85d94ec934dab7823c474efef1b62692 | p@chr5:152082403..152082408, + |
| 3.9e-69 | FFCP PHASE1:Hg19::chr5:152082403..152082408,+#_85d94ec934dab7823c474efef1b62692 | p@chr5:152082403..152082408, + |
| 6.26e-69 | FFCP PHASE2:Hg19::chr21:18811205..18811216,+#_a72d345ba2e4217f16055127d73c6ab7 | p3@C21orf37 |
| 6.26e-69 | FFCP PHASE1:Hg19::chr21:18811205..18811216,+#_a72d345ba2e4217f16055127d73c6ab7 | p3@C21orf37 |
| 7.27e-69 | FFCP PHASE2:Hg19::chr4:34621389..34621413,+#_9cd6c582a9ff8384404c33cfdcbab05c | p@chr4:34621389..34621413, + |
| 7.27e-69 | FFCP PHASE1:Hg19::chr4:34621389..34621413,+#_9cd6c582a9ff8384404c33cfdcbab05c | p@chr4:34621389..34621413, + |
| 1.46e-68 | FFCP PHASE1:Hg19::chrX:16753203..16753238,+#_aa3378aac3944bb422a3da8fd63a1204 | p@chrX:16753203..16753238, + |
| 1.46e-68 | FFCP PHASE2:Hg19::chrX:16753203..16753238,+#_aa3378aac3944bb422a3da8fd63a1204 | p@chrX:16753203..16753238, + |
| 1.47e-66 | FFCP PHASE1:Hg19::chr15:93616900..93616918,-#_15d312fbf39ad5233a3208aade390686 | p6@RGMA |
| 1.47e-66 | FFCP PHASE2:Hg19::chr15:93616900..93616918,-#_15d312fbf39ad5233a3208aade390686 | p6@RGMA |
| 1.87e-66 | FFCP PHASE2:Hg19::chr18:5577640..5577652,-#_43eddf22ed52394d9aaed4c2c7fd540d | p14@EPB41L3 |
| 1.87e-66 | FFCP PHASE1:Hg19::chr18:5577640..5577652,-#_43eddf22ed52394d9aaed4c2c7fd540d | p14@EPB41L3 |
| 2.06e-66 | FFCP PHASE1:Hg19::chr2:25720352..25720388,-#_e880f46bf4e87ab966374e9c57c59655 | p7@DTNB |
| 2.06e-66 | FFCP PHASE2:Hg19::chr2:25720352..25720388,-#_e880f46bf4e87ab966374e9c57c59655 | p7@DTNB |
| 2.83e-66 | FFCP PHASE2:Hg19::chr6:132580699..132580702,+#_2a2041befc4eada1b7dd8cbc01329371 | p@chr6:132580699..132580702, + |
| 2.83e-66 | FFCP PHASE1:Hg19::chr6:132580699..132580702,+#_2a2041befc4eada1b7dd8cbc01329371 | p@chr6:132580699..132580702, + |
| 2.83e-66 | FFCP PHASE1:Hg19::chr11:3224990..3225000,-#_2a2041befc4eada1b7dd8cbc01329371 | p@chr11:3224990..3225000, - |
| 2.83e-66 | FFCP PHASE2:Hg19::chr5:35090057..35090065,-#_2a2041befc4eada1b7dd8cbc01329371 | p27@PRLR |
| 2.83e-66 | FFCP PHASE2:Hg19::chr4:117675642..117675654,+#_2a2041befc4eada1b7dd8cbc01329371 | p@chr4:117675642..117675654, + |
| 2.83e-66 | FFCP PHASE1:Hg19::chr6:56820018..56820029,+#_2a2041befc4eada1b7dd8cbc01329371 | p16@BEND6 |
| 2.83e-66 | FFCP PHASE2:Hg19::chr12:33592574..33592584,-#_2a2041befc4eada1b7dd8cbc01329371 | p6@SYT10 |
| 2.83e-66 | FFCP PHASE1:Hg19::chr5:35090057..35090065,-#_2a2041befc4eada1b7dd8cbc01329371 | p27@PRLR |
| 2.83e-66 | FFCP PHASE2:Hg19::chr2:237146889..237146895,-#_2a2041befc4eada1b7dd8cbc01329371 | p@chr2:237146889..237146895, - |
| 2.83e-66 | FFCP PHASE1:Hg19::chr2:237146889..237146895,-#_2a2041befc4eada1b7dd8cbc01329371 | p@chr2:237146889..237146895, - |
| 2.83e-66 | FFCP PHASE1:Hg19::chr5:35090318..35090324,-#_2a2041befc4eada1b7dd8cbc01329371 | p@chr5:35090318..35090324, - |
| 2.83e-66 | FFCP PHASE1:Hg19::chr12:33592574..33592584,-#_2a2041befc4eada1b7dd8cbc01329371 | p6@SYT10 |
| 2.83e-66 | FFCP PHASE2:Hg19::chr6:56820018..56820029,+#_2a2041befc4eada1b7dd8cbc01329371 | p16@BEND6 |
| 2.83e-66 | FFCP PHASE1:Hg19::chr12:44467410..44467418,+#_2a2041befc4eada1b7dd8cbc01329371 | p13@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.
