UBERON:0001891

Name:	midbrain
Namespace:	FANTOM
Definition:	"Organ component of neuraxis that has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct[FMA]. The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally[ZFA]. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]." [FMA:61993, GO:0030901, Wikipedia:Midbrain, ZFIN:curator]
Xrefs:	Expandlinks: AAO:0010149 ABA:MB BM:MB BTO:0000138 EFO:0000919 EHDAA2:0001162 EHDAA:3694 EMAPA:16974 EV:0100242 FMA:61993 [1] [2] MA:0000207 MAT:0000106 MESH:A.08.186.211.132.659 MIAA:0000106 ncithesaurus:Mesencephalon NIF_GrossAnatomy:birnlex_1667 OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001104 SCTID:279099009 TAO:0000128 VHOG:0000069 XAO:0000014 ZFA:0000128
Synonyms:	"mesencephalon" RELATED LATIN [Wikipedia:Midbrain] "midbrain vesicle" RELATED []
Comments:	Editors note: developmental relationships need revised. AO notes: part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships
Alt_id:	UBERON:FMA_61993-MA_0000207-MIAA_0000106-XAO_0000014-ZFA_0000128
Subset:	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

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Parents

is_a:	UBERON:0002616(regional part of brain),UBERON:0010314(structure with developmental contribution from neural crest)
develops_from:	UBERON:0009616(presumptive midbrain)
part_of:	UBERON:0000955(brain)

Children

part of:	UBERON:0002038 (substantia nigra),UBERON:0002314 (midbrain tectum),UBERON:0002950 (regional part of midbrain),UBERON:0009661 (midbrain nucleus)

Ontology Tree: Loaded from BioPortal

Ontorolgy tree(Small window open)

FF samples<br>It includes FANTOM5 samples that overlay the Uberon ontology

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Human (Homo sapiens)

• 10158-103A5 (substantia nigra, adult, donor10252)
• 10178-103C7 (substantia nigra - adult, donor10196)
• 10358-105E7 (substantia nigra, newborn, donor10223)
• 10371-105G2 (substantia nigra, adult, donor10258)
• 11489-119E4 (Mouse Neurons - substantia nigra, donor4)
• 11490-119E5 (Mouse Neurons - substantia nigra, donor5)
• 11770-123I6 (Mouse Neurons - substantia nigra, donor6)
• 16-22A4 (corpora quadrigemina, adult)

Mouse (Mus musculus)

• 10158-103A5 (substantia nigra, adult, donor10252)
• 10178-103C7 (substantia nigra - adult, donor10196)
• 10358-105E7 (substantia nigra, newborn, donor10223)
• 10371-105G2 (substantia nigra, adult, donor10258)
• 11489-119E4 (Mouse Neurons - substantia nigra, donor4)
• 11490-119E5 (Mouse Neurons - substantia nigra, donor5)
• 11770-123I6 (Mouse Neurons - substantia nigra, donor6)
• 16-22A4 (corpora quadrigemina, adult)

Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with UBERON:0001891 (midbrain), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

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P-value	FFCP	Short description

P-value	FFCP	Short description
9.37e-99	FFCP PHASE1:Hg19::chr1:24915966..24915971,+	p5@C1orf130
9.37e-99	FFCP PHASE2:Hg19::chr1:24915966..24915971,+	p5@C1orf130
9.37e-99	FFCP PHASE2:Hg19::chr9:139916913..139916917,+	p@chr9:139916913..139916917, +
9.37e-99	FFCP PHASE2:Hg19::chr4:56229918..56229919,-	p@chr4:56229918..56229919, -
9.37e-99	FFCP PHASE1:Hg19::chr10:62149979..62149980,-	p59@ANK3
9.37e-99	FFCP PHASE2:Hg19::chr10:62149979..62149980,-	p59@ANK3
9.37e-99	FFCP PHASE1:Hg19::chr9:139916913..139916917,+	p@chr9:139916913..139916917, +
9.37e-99	FFCP PHASE1:Hg19::chr4:56229918..56229919,-	p@chr4:56229918..56229919, -
9.37e-99	FFCP PHASE1:Hg19::chr10:68718064..68718067,-	p@chr10:68718064..68718067, -
9.37e-99	FFCP PHASE2:Hg19::chr10:68718064..68718067,-	p@chr10:68718064..68718067, -
2.55e-98	FFCP PHASE2:Hg19::chr1:65776926..65776928,+	p@chr1:65776926..65776928, +
2.55e-98	FFCP PHASE1:Hg19::chr18:74702556..74702558,-	p@chr18:74702556..74702558, -
2.55e-98	FFCP PHASE1:Hg19::chr1:65776926..65776928,+	p@chr1:65776926..65776928, +
2.55e-98	FFCP PHASE2:Hg19::chr5:57935348..57935354,-	p@chr5:57935348..57935354, -
2.55e-98	FFCP PHASE2:Hg19::chr18:74702556..74702558,-	p@chr18:74702556..74702558, -
2.55e-98	FFCP PHASE1:Hg19::chr5:57935348..57935354,-	p@chr5:57935348..57935354, -
1.23e-66	FFCP PHASE2:Hg19::chr16:57309513..57309516,-	p@chr16:57309513..57309516, -
1.23e-66	FFCP PHASE2:Hg19::chr8:53312058..53312067,-	p@chr8:53312058..53312067, -
1.23e-66	FFCP PHASE2:Hg19::chr16:81170013..81170024,-	p6@PKD1L2
1.23e-66	FFCP PHASE1:Hg19::chr8:53312058..53312067,-	p@chr8:53312058..53312067, -
1.23e-66	FFCP PHASE1:Hg19::chr10:22967066..22967069,-	p@chr10:22967066..22967069, -
1.23e-66	FFCP PHASE1:Hg19::chr16:81170013..81170024,-	p6@PKD1L2
1.23e-66	FFCP PHASE2:Hg19::chr10:22967066..22967069,-	p@chr10:22967066..22967069, -
1.23e-66	FFCP PHASE1:Hg19::chr16:57309513..57309516,-	p@chr16:57309513..57309516, -
2.39e-66	FFCP PHASE1:Hg19::chr14:95727527..95727529,-	p@chr14:95727527..95727529, -
2.39e-66	FFCP PHASE2:Hg19::chr14:95727527..95727529,-	p@chr14:95727527..95727529, -
2.39e-66	FFCP PHASE2:Hg19::chr1:44956567..44956571,+	p@chr1:44956567..44956571, +
2.39e-66	FFCP PHASE2:Hg19::chr11:7340444..7340448,+	p@chr11:7340444..7340448, +
2.39e-66	FFCP PHASE1:Hg19::chr1:44956567..44956571,+	p@chr1:44956567..44956571, +
2.39e-66	FFCP PHASE1:Hg19::chr11:7340444..7340448,+	p@chr11:7340444..7340448, +
4.66e-66	FFCP PHASE2:Hg19::chr13:34922094..34922105,+	p@chr13:34922094..34922105, +
4.66e-66	FFCP PHASE1:Hg19::chr17:29623232..29623241,-	p8@OMG
4.66e-66	FFCP PHASE1:Hg19::chr13:34922094..34922105,+	p@chr13:34922094..34922105, +
4.66e-66	FFCP PHASE2:Hg19::chr9:79516011..79516022,-	p@chr9:79516011..79516022, -
4.66e-66	FFCP PHASE1:Hg19::chr14:105166013..105166017,+	p@chr14:105166013..105166017, +
4.66e-66	FFCP PHASE2:Hg19::chr14:105166013..105166017,+	p@chr14:105166013..105166017, +
4.66e-66	FFCP PHASE2:Hg19::chr17:29623232..29623241,-	p8@OMG
4.66e-66	FFCP PHASE2:Hg19::chr13:43872447..43872452,-	p@chr13:43872447..43872452, -
4.66e-66	FFCP PHASE1:Hg19::chr13:43872447..43872452,-	p@chr13:43872447..43872452, -
4.66e-66	FFCP PHASE1:Hg19::chr9:79516011..79516022,-	p@chr9:79516011..79516022, -
1.46e-50	FFCP PHASE2:Hg19::chr9:108178201..108178203,+	p@chr9:108178201..108178203, +
1.46e-50	FFCP PHASE1:Hg19::chr9:108178201..108178203,+	p@chr9:108178201..108178203, +
1.46e-50	FFCP PHASE2:Hg19::chrX:28627633..28627642,+	p@chrX:28627633..28627642, +
1.46e-50	FFCP PHASE1:Hg19::chrX:28627633..28627642,+	p@chrX:28627633..28627642, +
3.99e-50	FFCP PHASE2:Hg19::chr20:52570026..52570037,-	p@chr20:52570026..52570037, -
3.99e-50	FFCP PHASE1:Hg19::chr6:134626498..134626502,-	p@chr6:134626498..134626502, -
3.99e-50	FFCP PHASE1:Hg19::chr6:89803656..89803659,+	p@chr6:89803656..89803659, +
3.99e-50	FFCP PHASE2:Hg19::chr3:50717966..50717971,+	p@chr3:50717966..50717971, +
3.99e-50	FFCP PHASE1:Hg19::chr20:52570026..52570037,-	p@chr20:52570026..52570037, -
3.99e-50	FFCP PHASE2:Hg19::chr6:134626498..134626502,-	p@chr6:134626498..134626502, -
3.99e-50	FFCP PHASE1:Hg19::chr3:50717966..50717971,+	p@chr3:50717966..50717971, +
3.99e-50	FFCP PHASE2:Hg19::chr6:89803656..89803659,+	p@chr6:89803656..89803659, +
6.58e-50	FFCP PHASE2:Hg19::chr6:151042126..151042135,+	p21@PLEKHG1
6.58e-50	FFCP PHASE1:Hg19::chr6:163745521..163745530,-	p2@LOC285796
6.58e-50	FFCP PHASE1:Hg19::chr1:160009700..160009711,-	p10@KCNJ10
6.58e-50	FFCP PHASE2:Hg19::chr1:160009700..160009711,-	p10@KCNJ10
6.58e-50	FFCP PHASE1:Hg19::chr9:137240632..137240635,+	p@chr9:137240632..137240635, +
6.58e-50	FFCP PHASE2:Hg19::chr18:26665245..26665249,+	p@chr18:26665245..26665249, +
6.58e-50	FFCP PHASE2:Hg19::chr9:19515907..19515918,-	p@chr9:19515907..19515918, -
6.58e-50	FFCP PHASE2:Hg19::chr17:70910145..70910148,-	p@chr17:70910145..70910148, -
6.58e-50	FFCP PHASE2:Hg19::chr17:3479944..3479947,-	p@chr17:3479944..3479947, -
6.58e-50	FFCP PHASE1:Hg19::chr6:151042126..151042135,+	p21@PLEKHG1
6.58e-50	FFCP PHASE2:Hg19::chr22:48980473..48980481,+	p@chr22:48980473..48980481, +
6.58e-50	FFCP PHASE1:Hg19::chr18:26665245..26665249,+	p@chr18:26665245..26665249, +
6.58e-50	FFCP PHASE1:Hg19::chr17:70910145..70910148,-	p@chr17:70910145..70910148, -
6.58e-50	FFCP PHASE1:Hg19::chr17:3479944..3479947,-	p@chr17:3479944..3479947, -
6.58e-50	FFCP PHASE2:Hg19::chr1:161275096..161275109,-	p@chr1:161275096..161275109, -
6.58e-50	FFCP PHASE2:Hg19::chr6:163745521..163745530,-	p2@LOC285796
6.58e-50	FFCP PHASE1:Hg19::chr1:161275096..161275109,-	p@chr1:161275096..161275109, -
6.58e-50	FFCP PHASE1:Hg19::chr9:19515907..19515918,-	p@chr9:19515907..19515918, -
6.58e-50	FFCP PHASE2:Hg19::chr9:137240632..137240635,+	p@chr9:137240632..137240635, +
6.58e-50	FFCP PHASE1:Hg19::chr22:48980473..48980481,+	p@chr22:48980473..48980481, +
2.38e-43	FFCP PHASE1:Mm9::chr19:40804786..40804795,-	p@chr19:40804786..40804795, -
2.38e-43	FFCP PHASE2:Mm9::chr19:40804786..40804795,-	p@chr19:40804786..40804795, -
6.62e-41	FFCP PHASE1:Hg19::chr5:60933634..60933637,+	p4@C5orf64
6.62e-41	FFCP PHASE2:Hg19::chr4:139891920..139891924,-	p@chr4:139891920..139891924, -
6.62e-41	FFCP PHASE1:Hg19::chr4:139891920..139891924,-	p@chr4:139891920..139891924, -
6.62e-41	FFCP PHASE2:Hg19::chr5:60933634..60933637,+	p4@C5orf64
9.91e-41	FFCP PHASE1:Hg19::chr13:21100208..21100214,+	p@chr13:21100208..21100214, +
9.91e-41	FFCP PHASE1:Hg19::chr5:152017019..152017026,+	p@chr5:152017019..152017026, +
9.91e-41	FFCP PHASE2:Hg19::chr13:21100208..21100214,+	p@chr13:21100208..21100214, +
9.91e-41	FFCP PHASE2:Hg19::chrX:13792462..13792477,-	p@chrX:13792462..13792477, -
9.91e-41	FFCP PHASE2:Hg19::chr5:152017019..152017026,+	p@chr5:152017019..152017026, +
9.91e-41	FFCP PHASE1:Hg19::chrX:13792462..13792477,-	p@chrX:13792462..13792477, -
1.48e-40	FFCP PHASE2:Hg19::chr9:139911084..139911102,-	p@chr9:139911084..139911102, -
1.48e-40	FFCP PHASE2:Hg19::chr17:71046459..71046462,-	p@chr17:71046459..71046462, -
1.48e-40	FFCP PHASE2:Hg19::chr2:135170207..135170218,+	p@chr2:135170207..135170218, +
1.48e-40	FFCP PHASE1:Hg19::chr9:139911084..139911102,-	p@chr9:139911084..139911102, -
1.48e-40	FFCP PHASE1:Hg19::chr17:71046459..71046462,-	p@chr17:71046459..71046462, -
1.48e-40	FFCP PHASE2:Hg19::chr1:161275238..161275250,-	p@chr1:161275238..161275250, -
1.48e-40	FFCP PHASE1:Hg19::chr1:161275238..161275250,-	p@chr1:161275238..161275250, -
1.48e-40	FFCP PHASE1:Hg19::chr2:135170207..135170218,+	p@chr2:135170207..135170218, +
1.48e-40	FFCP PHASE1:Hg19::chr1:109806865..109806872,+	p10@CELSR2
1.48e-40	FFCP PHASE2:Hg19::chr1:109806865..109806872,+	p10@CELSR2
2.21e-40	FFCP PHASE1:Hg19::chr8:27522642..27522647,+	p@chr8:27522642..27522647, +
2.21e-40	FFCP PHASE1:Hg19::chr9:19513297..19513309,-	p4@SLC24A2
2.21e-40	FFCP PHASE1:Hg19::chr10:1246202..1246207,-	p19@ADARB2
2.21e-40	FFCP PHASE2:Hg19::chr10:1246202..1246207,-	p19@ADARB2
2.21e-40	FFCP PHASE2:Hg19::chr8:27522642..27522647,+	p@chr8:27522642..27522647, +
2.21e-40	FFCP PHASE2:Hg19::chrX:103046993..103046994,+	p@chrX:103046993..103046994, +

Showing 1 to 100 of 100 entries

Property "Property value" (as page type) with input value "UBPROP:0000001 "Middle part of the brain composed of the optic tectum and penducular region.[AAO]" xsd:string" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process., Property "Property value" (as page type) with input value "UBPROP:0000001 "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]" xsd:string" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.