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UBERON:0001891

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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:
links:

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

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

Human (Homo sapiens)

Mouse (Mus musculus)


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

P-valueFFCPShort description
9.37e-99FFCP PHASE1:Hg19::chr4:56229918..56229919,-#_4bb36d079a358f3efb467285a481d68fp@chr4:56229918..56229919, -
9.37e-99FFCP PHASE2:Hg19::chr4:56229918..56229919,-#_4bb36d079a358f3efb467285a481d68fp@chr4:56229918..56229919, -
9.37e-99FFCP PHASE2:Hg19::chr10:68718064..68718067,-#_4bb36d079a358f3efb467285a481d68fp@chr10:68718064..68718067, -
9.37e-99FFCP PHASE1:Hg19::chr10:62149979..62149980,-#_4bb36d079a358f3efb467285a481d68fp59@ANK3
9.37e-99FFCP PHASE2:Hg19::chr1:24915966..24915971,+#_4bb36d079a358f3efb467285a481d68fp5@C1orf130
9.37e-99FFCP PHASE1:Hg19::chr1:24915966..24915971,+#_4bb36d079a358f3efb467285a481d68fp5@C1orf130
9.37e-99FFCP PHASE1:Hg19::chr10:68718064..68718067,-#_4bb36d079a358f3efb467285a481d68fp@chr10:68718064..68718067, -
9.37e-99FFCP PHASE2:Hg19::chr10:62149979..62149980,-#_4bb36d079a358f3efb467285a481d68fp59@ANK3
9.37e-99FFCP PHASE1:Hg19::chr9:139916913..139916917,+#_4bb36d079a358f3efb467285a481d68fp@chr9:139916913..139916917, +
9.37e-99FFCP PHASE2:Hg19::chr9:139916913..139916917,+#_4bb36d079a358f3efb467285a481d68fp@chr9:139916913..139916917, +
2.55e-98FFCP PHASE2:Hg19::chr18:74702556..74702558,-#_1c887a12805d57770e877d86b51bf8d9p@chr18:74702556..74702558, -
2.55e-98FFCP PHASE2:Hg19::chr5:57935348..57935354,-#_1c887a12805d57770e877d86b51bf8d9p@chr5:57935348..57935354, -
2.55e-98FFCP PHASE1:Hg19::chr5:57935348..57935354,-#_1c887a12805d57770e877d86b51bf8d9p@chr5:57935348..57935354, -
2.55e-98FFCP PHASE2:Hg19::chr1:65776926..65776928,+#_1c887a12805d57770e877d86b51bf8d9p@chr1:65776926..65776928, +
2.55e-98FFCP PHASE1:Hg19::chr18:74702556..74702558,-#_1c887a12805d57770e877d86b51bf8d9p@chr18:74702556..74702558, -
2.55e-98FFCP PHASE1:Hg19::chr1:65776926..65776928,+#_1c887a12805d57770e877d86b51bf8d9p@chr1:65776926..65776928, +
1.23e-66FFCP PHASE1:Hg19::chr16:81170013..81170024,-#_3a917a84f9dc9b11b8639df82e9bf914p6@PKD1L2
1.23e-66FFCP PHASE2:Hg19::chr10:22967066..22967069,-#_3a917a84f9dc9b11b8639df82e9bf914p@chr10:22967066..22967069, -
1.23e-66FFCP PHASE1:Hg19::chr16:57309513..57309516,-#_3a917a84f9dc9b11b8639df82e9bf914p@chr16:57309513..57309516, -
1.23e-66FFCP PHASE2:Hg19::chr16:57309513..57309516,-#_3a917a84f9dc9b11b8639df82e9bf914p@chr16:57309513..57309516, -
1.23e-66FFCP PHASE1:Hg19::chr10:22967066..22967069,-#_3a917a84f9dc9b11b8639df82e9bf914p@chr10:22967066..22967069, -
1.23e-66FFCP PHASE2:Hg19::chr16:81170013..81170024,-#_3a917a84f9dc9b11b8639df82e9bf914p6@PKD1L2
1.23e-66FFCP PHASE2:Hg19::chr8:53312058..53312067,-#_3a917a84f9dc9b11b8639df82e9bf914p@chr8:53312058..53312067, -
1.23e-66FFCP PHASE1:Hg19::chr8:53312058..53312067,-#_3a917a84f9dc9b11b8639df82e9bf914p@chr8:53312058..53312067, -
2.39e-66FFCP PHASE1:Hg19::chr11:7340444..7340448,+#_e883a6df184d15b6421145a949ae13a0p@chr11:7340444..7340448, +
2.39e-66FFCP PHASE1:Hg19::chr14:95727527..95727529,-#_e883a6df184d15b6421145a949ae13a0p@chr14:95727527..95727529, -
2.39e-66FFCP PHASE2:Hg19::chr14:95727527..95727529,-#_e883a6df184d15b6421145a949ae13a0p@chr14:95727527..95727529, -
2.39e-66FFCP PHASE2:Hg19::chr1:44956567..44956571,+#_e883a6df184d15b6421145a949ae13a0p@chr1:44956567..44956571, +
2.39e-66FFCP PHASE2:Hg19::chr11:7340444..7340448,+#_e883a6df184d15b6421145a949ae13a0p@chr11:7340444..7340448, +
2.39e-66FFCP PHASE1:Hg19::chr1:44956567..44956571,+#_e883a6df184d15b6421145a949ae13a0p@chr1:44956567..44956571, +
4.66e-66FFCP PHASE2:Hg19::chr17:29623232..29623241,-#_a923a0027fa79b41f5fb2827c364276cp8@OMG
4.66e-66FFCP PHASE2:Hg19::chr13:43872447..43872452,-#_a923a0027fa79b41f5fb2827c364276cp@chr13:43872447..43872452, -
4.66e-66FFCP PHASE1:Hg19::chr13:43872447..43872452,-#_a923a0027fa79b41f5fb2827c364276cp@chr13:43872447..43872452, -
4.66e-66FFCP PHASE1:Hg19::chr9:79516011..79516022,-#_a923a0027fa79b41f5fb2827c364276cp@chr9:79516011..79516022, -
4.66e-66FFCP PHASE2:Hg19::chr13:34922094..34922105,+#_a923a0027fa79b41f5fb2827c364276cp@chr13:34922094..34922105, +
4.66e-66FFCP PHASE1:Hg19::chr17:29623232..29623241,-#_a923a0027fa79b41f5fb2827c364276cp8@OMG
4.66e-66FFCP PHASE1:Hg19::chr13:34922094..34922105,+#_a923a0027fa79b41f5fb2827c364276cp@chr13:34922094..34922105, +
4.66e-66FFCP PHASE1:Hg19::chr14:105166013..105166017,+#_a923a0027fa79b41f5fb2827c364276cp@chr14:105166013..105166017, +
4.66e-66FFCP PHASE2:Hg19::chr14:105166013..105166017,+#_a923a0027fa79b41f5fb2827c364276cp@chr14:105166013..105166017, +
4.66e-66FFCP PHASE2:Hg19::chr9:79516011..79516022,-#_a923a0027fa79b41f5fb2827c364276cp@chr9:79516011..79516022, -
1.46e-50FFCP PHASE1:Hg19::chrX:28627633..28627642,+#_e92a00d69d3d1c12dbae63f3900bf6fbp@chrX:28627633..28627642, +
1.46e-50FFCP PHASE2:Hg19::chrX:28627633..28627642,+#_e92a00d69d3d1c12dbae63f3900bf6fbp@chrX:28627633..28627642, +
1.46e-50FFCP PHASE1:Hg19::chr9:108178201..108178203,+#_e92a00d69d3d1c12dbae63f3900bf6fbp@chr9:108178201..108178203, +
1.46e-50FFCP PHASE2:Hg19::chr9:108178201..108178203,+#_e92a00d69d3d1c12dbae63f3900bf6fbp@chr9:108178201..108178203, +
3.99e-50FFCP PHASE1:Hg19::chr3:50717966..50717971,+#_08ad9d1d97f2644b4eb609927c9d4c19p@chr3:50717966..50717971, +
3.99e-50FFCP PHASE2:Hg19::chr3:50717966..50717971,+#_08ad9d1d97f2644b4eb609927c9d4c19p@chr3:50717966..50717971, +
3.99e-50FFCP PHASE2:Hg19::chr6:134626498..134626502,-#_08ad9d1d97f2644b4eb609927c9d4c19p@chr6:134626498..134626502, -
3.99e-50FFCP PHASE1:Hg19::chr6:134626498..134626502,-#_08ad9d1d97f2644b4eb609927c9d4c19p@chr6:134626498..134626502, -
3.99e-50FFCP PHASE1:Hg19::chr6:89803656..89803659,+#_08ad9d1d97f2644b4eb609927c9d4c19p@chr6:89803656..89803659, +
3.99e-50FFCP PHASE2:Hg19::chr6:89803656..89803659,+#_08ad9d1d97f2644b4eb609927c9d4c19p@chr6:89803656..89803659, +
3.99e-50FFCP PHASE1:Hg19::chr20:52570026..52570037,-#_08ad9d1d97f2644b4eb609927c9d4c19p@chr20:52570026..52570037, -
3.99e-50FFCP PHASE2:Hg19::chr20:52570026..52570037,-#_08ad9d1d97f2644b4eb609927c9d4c19p@chr20:52570026..52570037, -
6.58e-50FFCP PHASE2:Hg19::chr9:19515907..19515918,-#_44bf015a558107f1b76ee1383a5287edp@chr9:19515907..19515918, -
6.58e-50FFCP PHASE1:Hg19::chr17:70910145..70910148,-#_44bf015a558107f1b76ee1383a5287edp@chr17:70910145..70910148, -
6.58e-50FFCP PHASE1:Hg19::chr17:3479944..3479947,-#_44bf015a558107f1b76ee1383a5287edp@chr17:3479944..3479947, -
6.58e-50FFCP PHASE1:Hg19::chr1:161275096..161275109,-#_44bf015a558107f1b76ee1383a5287edp@chr1:161275096..161275109, -
6.58e-50FFCP PHASE1:Hg19::chr9:19515907..19515918,-#_44bf015a558107f1b76ee1383a5287edp@chr9:19515907..19515918, -
6.58e-50FFCP PHASE2:Hg19::chr1:161275096..161275109,-#_44bf015a558107f1b76ee1383a5287edp@chr1:161275096..161275109, -
6.58e-50FFCP PHASE1:Hg19::chr22:48980473..48980481,+#_44bf015a558107f1b76ee1383a5287edp@chr22:48980473..48980481, +
6.58e-50FFCP PHASE2:Hg19::chr22:48980473..48980481,+#_44bf015a558107f1b76ee1383a5287edp@chr22:48980473..48980481, +
6.58e-50FFCP PHASE1:Hg19::chr6:163745521..163745530,-#_44bf015a558107f1b76ee1383a5287edp2@LOC285796
6.58e-50FFCP PHASE2:Hg19::chr6:163745521..163745530,-#_44bf015a558107f1b76ee1383a5287edp2@LOC285796
6.58e-50FFCP PHASE1:Hg19::chr1:160009700..160009711,-#_44bf015a558107f1b76ee1383a5287edp10@KCNJ10
6.58e-50FFCP PHASE2:Hg19::chr1:160009700..160009711,-#_44bf015a558107f1b76ee1383a5287edp10@KCNJ10
6.58e-50FFCP PHASE1:Hg19::chr9:137240632..137240635,+#_44bf015a558107f1b76ee1383a5287edp@chr9:137240632..137240635, +
6.58e-50FFCP PHASE2:Hg19::chr9:137240632..137240635,+#_44bf015a558107f1b76ee1383a5287edp@chr9:137240632..137240635, +
6.58e-50FFCP PHASE2:Hg19::chr18:26665245..26665249,+#_44bf015a558107f1b76ee1383a5287edp@chr18:26665245..26665249, +
6.58e-50FFCP PHASE2:Hg19::chr6:151042126..151042135,+#_44bf015a558107f1b76ee1383a5287edp21@PLEKHG1
6.58e-50FFCP PHASE2:Hg19::chr17:70910145..70910148,-#_44bf015a558107f1b76ee1383a5287edp@chr17:70910145..70910148, -
6.58e-50FFCP PHASE2:Hg19::chr17:3479944..3479947,-#_44bf015a558107f1b76ee1383a5287edp@chr17:3479944..3479947, -
6.58e-50FFCP PHASE1:Hg19::chr6:151042126..151042135,+#_44bf015a558107f1b76ee1383a5287edp21@PLEKHG1
6.58e-50FFCP PHASE1:Hg19::chr18:26665245..26665249,+#_44bf015a558107f1b76ee1383a5287edp@chr18:26665245..26665249, +
2.38e-43FFCP PHASE1:Mm9::chr19:40804786..40804795,-#_3838eb3243f02c74b4aa6452bcc4ca2dp@chr19:40804786..40804795, -
2.38e-43FFCP PHASE2:Mm9::chr19:40804786..40804795,-#_3838eb3243f02c74b4aa6452bcc4ca2dp@chr19:40804786..40804795, -
6.62e-41FFCP PHASE2:Hg19::chr5:60933634..60933637,+#_e77f54ed2f3411eebba5b85c38e26037p4@C5orf64
6.62e-41FFCP PHASE1:Hg19::chr5:60933634..60933637,+#_e77f54ed2f3411eebba5b85c38e26037p4@C5orf64
6.62e-41FFCP PHASE2:Hg19::chr4:139891920..139891924,-#_e77f54ed2f3411eebba5b85c38e26037p@chr4:139891920..139891924, -
6.62e-41FFCP PHASE1:Hg19::chr4:139891920..139891924,-#_e77f54ed2f3411eebba5b85c38e26037p@chr4:139891920..139891924, -
9.91e-41FFCP PHASE1:Hg19::chrX:13792462..13792477,-#_30051241114b8a677c0f197c3372a7a2p@chrX:13792462..13792477, -
9.91e-41FFCP PHASE2:Hg19::chrX:13792462..13792477,-#_30051241114b8a677c0f197c3372a7a2p@chrX:13792462..13792477, -
9.91e-41FFCP PHASE1:Hg19::chr13:21100208..21100214,+#_30051241114b8a677c0f197c3372a7a2p@chr13:21100208..21100214, +
9.91e-41FFCP PHASE1:Hg19::chr5:152017019..152017026,+#_30051241114b8a677c0f197c3372a7a2p@chr5:152017019..152017026, +
9.91e-41FFCP PHASE2:Hg19::chr5:152017019..152017026,+#_30051241114b8a677c0f197c3372a7a2p@chr5:152017019..152017026, +
9.91e-41FFCP PHASE2:Hg19::chr13:21100208..21100214,+#_30051241114b8a677c0f197c3372a7a2p@chr13:21100208..21100214, +
1.48e-40FFCP PHASE2:Hg19::chr1:109806865..109806872,+#_40281736166578a191fcacd2e1b6f2a3p10@CELSR2
1.48e-40FFCP PHASE1:Hg19::chr1:109806865..109806872,+#_40281736166578a191fcacd2e1b6f2a3p10@CELSR2
1.48e-40FFCP PHASE2:Hg19::chr17:71046459..71046462,-#_40281736166578a191fcacd2e1b6f2a3p@chr17:71046459..71046462, -
1.48e-40FFCP PHASE1:Hg19::chr9:139911084..139911102,-#_40281736166578a191fcacd2e1b6f2a3p@chr9:139911084..139911102, -
1.48e-40FFCP PHASE2:Hg19::chr9:139911084..139911102,-#_40281736166578a191fcacd2e1b6f2a3p@chr9:139911084..139911102, -
1.48e-40FFCP PHASE1:Hg19::chr17:71046459..71046462,-#_40281736166578a191fcacd2e1b6f2a3p@chr17:71046459..71046462, -
1.48e-40FFCP PHASE1:Hg19::chr1:161275238..161275250,-#_40281736166578a191fcacd2e1b6f2a3p@chr1:161275238..161275250, -
1.48e-40FFCP PHASE2:Hg19::chr1:161275238..161275250,-#_40281736166578a191fcacd2e1b6f2a3p@chr1:161275238..161275250, -
1.48e-40FFCP PHASE1:Hg19::chr2:135170207..135170218,+#_40281736166578a191fcacd2e1b6f2a3p@chr2:135170207..135170218, +
1.48e-40FFCP PHASE2:Hg19::chr2:135170207..135170218,+#_40281736166578a191fcacd2e1b6f2a3p@chr2:135170207..135170218, +
2.21e-40FFCP PHASE2:Hg19::chr8:27522642..27522647,+#_881117f3d03a5e7eba96cfe2186a09e6p@chr8:27522642..27522647, +
2.21e-40FFCP PHASE1:Hg19::chrX:103046993..103046994,+#_881117f3d03a5e7eba96cfe2186a09e6p@chrX:103046993..103046994, +
2.21e-40FFCP PHASE2:Hg19::chrX:103046993..103046994,+#_881117f3d03a5e7eba96cfe2186a09e6p@chrX:103046993..103046994, +
2.21e-40FFCP PHASE1:Hg19::chr10:1246202..1246207,-#_881117f3d03a5e7eba96cfe2186a09e6p19@ADARB2
2.21e-40FFCP PHASE1:Hg19::chr8:27522642..27522647,+#_881117f3d03a5e7eba96cfe2186a09e6p@chr8:27522642..27522647, +
2.21e-40FFCP PHASE1:Hg19::chr10:1246245..1246252,-#_881117f3d03a5e7eba96cfe2186a09e6p20@ADARB2










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.

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