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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
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)
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


FF samples
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
Analyst: Hideya Kawaji

link to source dataset
human : data
mouse : data


P-valueFFCPShort description
9.37e-99FFCP PHASE1:Hg19::chr4:56229918..56229919,-#_4bb36d079a358f3efb467285a481d68fp@chr4:56229918..56229919, -
9.37e-99FFCP PHASE2:Hg19::chr9:139916913..139916917,+#_4bb36d079a358f3efb467285a481d68f+, p@chr9:139916913..139916917
9.37e-99FFCP PHASE2:Hg19::chr10:68718064..68718067,-#_4bb36d079a358f3efb467285a481d68fp@chr10:68718064..68718067, -
9.37e-99FFCP PHASE1:Hg19::chr1:24915966..24915971,+#_4bb36d079a358f3efb467285a481d68fp5@C1orf130
9.37e-99FFCP PHASE1:Hg19::chr10:62149979..62149980,-#_4bb36d079a358f3efb467285a481d68fp59@ANK3
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::chr4:56229918..56229919,-#_4bb36d079a358f3efb467285a481d68fp@chr4:56229918..56229919, -
9.37e-99FFCP PHASE1:Hg19::chr10:68718064..68718067,-#_4bb36d079a358f3efb467285a481d68fp@chr10:68718064..68718067, -
9.37e-99FFCP PHASE2:Hg19::chr1:24915966..24915971,+#_4bb36d079a358f3efb467285a481d68fp5@C1orf130
2.55e-98FFCP PHASE1:Hg19::chr5:57935348..57935354,-#_1c887a12805d57770e877d86b51bf8d9p@chr5:57935348..57935354, -
2.55e-98FFCP PHASE2:Hg19::chr5:57935348..57935354,-#_1c887a12805d57770e877d86b51bf8d9p@chr5:57935348..57935354, -
2.55e-98FFCP PHASE1:Hg19::chr1:65776926..65776928,+#_1c887a12805d57770e877d86b51bf8d9p@chr1:65776926..65776928, +
2.55e-98FFCP PHASE1:Hg19::chr18:74702556..74702558,-#_1c887a12805d57770e877d86b51bf8d9p@chr18:74702556..74702558, -
2.55e-98FFCP PHASE2:Hg19::chr1:65776926..65776928,+#_1c887a12805d57770e877d86b51bf8d9p@chr1:65776926..65776928, +
2.55e-98FFCP PHASE2:Hg19::chr18:74702556..74702558,-#_1c887a12805d57770e877d86b51bf8d9p@chr18:74702556..74702558, -
1.23e-66FFCP PHASE1:Hg19::chr8:53312058..53312067,-#_3a917a84f9dc9b11b8639df82e9bf914p@chr8:53312058..53312067, -
1.23e-66FFCP PHASE1:Hg19::chr16:81170013..81170024,-#_3a917a84f9dc9b11b8639df82e9bf914p6@PKD1L2
1.23e-66FFCP PHASE2:Hg19::chr16:57309513..57309516,-#_3a917a84f9dc9b11b8639df82e9bf914p@chr16:57309513..57309516, -
1.23e-66FFCP PHASE1: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::chr10:22967066..22967069,-#_3a917a84f9dc9b11b8639df82e9bf914p@chr10:22967066..22967069, -
1.23e-66FFCP PHASE2:Hg19::chr8:53312058..53312067,-#_3a917a84f9dc9b11b8639df82e9bf914p@chr8:53312058..53312067, -
1.23e-66FFCP PHASE2:Hg19::chr16:81170013..81170024,-#_3a917a84f9dc9b11b8639df82e9bf914p6@PKD1L2
2.39e-66FFCP PHASE1:Hg19::chr1:44956567..44956571,+#_e883a6df184d15b6421145a949ae13a0p@chr1:44956567..44956571, +
2.39e-66FFCP PHASE1:Hg19::chr11:7340444..7340448,+#_e883a6df184d15b6421145a949ae13a0p@chr11:7340444..7340448, +
2.39e-66FFCP PHASE2:Hg19::chr11:7340444..7340448,+#_e883a6df184d15b6421145a949ae13a0p@chr11:7340444..7340448, +
2.39e-66FFCP PHASE2:Hg19::chr1:44956567..44956571,+#_e883a6df184d15b6421145a949ae13a0p@chr1:44956567..44956571, +
2.39e-66FFCP PHASE1:Hg19::chr14:95727527..95727529,-#_e883a6df184d15b6421145a949ae13a0p@chr14:95727527..95727529, -
2.39e-66FFCP PHASE2:Hg19::chr14:95727527..95727529,-#_e883a6df184d15b6421145a949ae13a0p@chr14:95727527..95727529, -
4.66e-66FFCP PHASE1:Hg19::chr9:79516011..79516022,-#_a923a0027fa79b41f5fb2827c364276cp@chr9:79516011..79516022, -
4.66e-66FFCP PHASE2:Hg19::chr13:43872447..43872452,-#_a923a0027fa79b41f5fb2827c364276cp@chr13:43872447..43872452, -
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 PHASE1:Hg19::chr13:43872447..43872452,-#_a923a0027fa79b41f5fb2827c364276cp@chr13:43872447..43872452, -
4.66e-66FFCP PHASE1:Hg19::chr17:29623232..29623241,-#_a923a0027fa79b41f5fb2827c364276cp8@OMG
4.66e-66FFCP PHASE2: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::chr13:34922094..34922105,+#_a923a0027fa79b41f5fb2827c364276cp@chr13:34922094..34922105, +
4.66e-66FFCP PHASE2:Hg19::chr17:29623232..29623241,-#_a923a0027fa79b41f5fb2827c364276cp8@OMG
1.46e-50FFCP PHASE2:Hg19::chrX:28627633..28627642,+#_e92a00d69d3d1c12dbae63f3900bf6fbp@chrX:28627633..28627642, +
1.46e-50FFCP PHASE2:Hg19::chr9:108178201..108178203,+#_e92a00d69d3d1c12dbae63f3900bf6fbp@chr9:108178201..108178203, +
1.46e-50FFCP PHASE1:Hg19::chrX:28627633..28627642,+#_e92a00d69d3d1c12dbae63f3900bf6fbp@chrX:28627633..28627642, +
1.46e-50FFCP PHASE1:Hg19::chr9:108178201..108178203,+#_e92a00d69d3d1c12dbae63f3900bf6fbp@chr9:108178201..108178203, +
3.99e-50FFCP PHASE2:Hg19::chr3:50717966..50717971,+#_08ad9d1d97f2644b4eb609927c9d4c19p@chr3:50717966..50717971, +
3.99e-50FFCP PHASE2:Hg19::chr20:52570026..52570037,-#_08ad9d1d97f2644b4eb609927c9d4c19p@chr20:52570026..52570037, -
3.99e-50FFCP PHASE1:Hg19::chr6:134626498..134626502,-#_08ad9d1d97f2644b4eb609927c9d4c19p@chr6:134626498..134626502, -
3.99e-50FFCP PHASE1:Hg19::chr3:50717966..50717971,+#_08ad9d1d97f2644b4eb609927c9d4c19+, p@chr3:50717966..50717971
3.99e-50FFCP PHASE1: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::chr6:134626498..134626502,-#_08ad9d1d97f2644b4eb609927c9d4c19p@chr6:134626498..134626502, -
3.99e-50FFCP PHASE2:Hg19::chr6:89803656..89803659,+#_08ad9d1d97f2644b4eb609927c9d4c19p@chr6:89803656..89803659, +
6.58e-50FFCP PHASE2:Hg19::chr9:137240632..137240635,+#_44bf015a558107f1b76ee1383a5287edp@chr9:137240632..137240635, +
6.58e-50FFCP PHASE1:Hg19::chr9:137240632..137240635,+#_44bf015a558107f1b76ee1383a5287edp@chr9:137240632..137240635, +
6.58e-50FFCP PHASE2:Hg19::chr1:161275096..161275109,-#_44bf015a558107f1b76ee1383a5287ed-, p@chr1:161275096..161275109
6.58e-50FFCP PHASE2:Hg19::chr18:26665245..26665249,+#_44bf015a558107f1b76ee1383a5287edp@chr18:26665245..26665249, +
6.58e-50FFCP PHASE1:Hg19::chr17:70910145..70910148,-#_44bf015a558107f1b76ee1383a5287edp@chr17:70910145..70910148, -
6.58e-50FFCP PHASE2:Hg19::chr6:151042126..151042135,+#_44bf015a558107f1b76ee1383a5287edp21@PLEKHG1
6.58e-50FFCP PHASE1:Hg19::chr17:3479944..3479947,-#_44bf015a558107f1b76ee1383a5287edp@chr17:3479944..3479947, -
6.58e-50FFCP PHASE1:Hg19::chr1:160009700..160009711,-#_44bf015a558107f1b76ee1383a5287edp10@KCNJ10
6.58e-50FFCP PHASE1:Hg19::chr6:163745521..163745530,-#_44bf015a558107f1b76ee1383a5287edp2@LOC285796
6.58e-50FFCP PHASE1:Hg19::chr9:19515907..19515918,-#_44bf015a558107f1b76ee1383a5287edp@chr9:19515907..19515918, -
6.58e-50FFCP PHASE2:Hg19::chr22:48980473..48980481,+#_44bf015a558107f1b76ee1383a5287edp@chr22:48980473..48980481, +
6.58e-50FFCP PHASE2:Hg19::chr17:3479944..3479947,-#_44bf015a558107f1b76ee1383a5287ed-, p@chr17:3479944..3479947
6.58e-50FFCP PHASE2:Hg19::chr6:163745521..163745530,-#_44bf015a558107f1b76ee1383a5287edp2@LOC285796
6.58e-50FFCP PHASE1:Hg19::chr6:151042126..151042135,+#_44bf015a558107f1b76ee1383a5287edp21@PLEKHG1
6.58e-50FFCP PHASE2:Hg19::chr17:70910145..70910148,-#_44bf015a558107f1b76ee1383a5287edp@chr17:70910145..70910148, -
6.58e-50FFCP PHASE2:Hg19::chr9:19515907..19515918,-#_44bf015a558107f1b76ee1383a5287edp@chr9:19515907..19515918, -
6.58e-50FFCP PHASE1:Hg19::chr22:48980473..48980481,+#_44bf015a558107f1b76ee1383a5287edp@chr22:48980473..48980481, +
6.58e-50FFCP PHASE1:Hg19::chr1:161275096..161275109,-#_44bf015a558107f1b76ee1383a5287edp@chr1:161275096..161275109, -
6.58e-50FFCP PHASE1:Hg19::chr18:26665245..26665249,+#_44bf015a558107f1b76ee1383a5287edp@chr18:26665245..26665249, +
6.58e-50FFCP PHASE2:Hg19::chr1:160009700..160009711,-#_44bf015a558107f1b76ee1383a5287edp10@KCNJ10
2.38e-43FFCP PHASE2:Mm9::chr19:40804786..40804795,-#_3838eb3243f02c74b4aa6452bcc4ca2dp@chr19:40804786..40804795, -
2.38e-43FFCP PHASE1: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 PHASE2:Hg19::chr5:152017019..152017026,+#_30051241114b8a677c0f197c3372a7a2p@chr5:152017019..152017026, +
9.91e-41FFCP PHASE1:Hg19::chr5:152017019..152017026,+#_30051241114b8a677c0f197c3372a7a2p@chr5:152017019..152017026, +
9.91e-41FFCP PHASE2:Hg19::chrX:13792462..13792477,-#_30051241114b8a677c0f197c3372a7a2p@chrX:13792462..13792477, -
9.91e-41FFCP PHASE1:Hg19::chrX:13792462..13792477,-#_30051241114b8a677c0f197c3372a7a2p@chrX:13792462..13792477, -
9.91e-41FFCP PHASE2:Hg19::chr13:21100208..21100214,+#_30051241114b8a677c0f197c3372a7a2p@chr13:21100208..21100214, +
9.91e-41FFCP PHASE1:Hg19::chr13:21100208..21100214,+#_30051241114b8a677c0f197c3372a7a2p@chr13:21100208..21100214, +
1.48e-40FFCP PHASE1:Hg19::chr1:109806865..109806872,+#_40281736166578a191fcacd2e1b6f2a3p10@CELSR2
1.48e-40FFCP PHASE1:Hg19::chr9:139911084..139911102,-#_40281736166578a191fcacd2e1b6f2a3p@chr9:139911084..139911102, -
1.48e-40FFCP PHASE2:Hg19::chr2:135170207..135170218,+#_40281736166578a191fcacd2e1b6f2a3p@chr2:135170207..135170218, +
1.48e-40FFCP PHASE1:Hg19::chr2:135170207..135170218,+#_40281736166578a191fcacd2e1b6f2a3p@chr2:135170207..135170218, +
1.48e-40FFCP PHASE2:Hg19::chr9:139911084..139911102,-#_40281736166578a191fcacd2e1b6f2a3-, p@chr9:139911084..139911102
1.48e-40FFCP PHASE1:Hg19::chr1:161275238..161275250,-#_40281736166578a191fcacd2e1b6f2a3p@chr1:161275238..161275250, -
1.48e-40FFCP PHASE2:Hg19::chr17:71046459..71046462,-#_40281736166578a191fcacd2e1b6f2a3p@chr17:71046459..71046462, -
1.48e-40FFCP PHASE2:Hg19::chr1:161275238..161275250,-#_40281736166578a191fcacd2e1b6f2a3p@chr1:161275238..161275250, -
1.48e-40FFCP PHASE1:Hg19::chr17:71046459..71046462,-#_40281736166578a191fcacd2e1b6f2a3p@chr17:71046459..71046462, -
1.48e-40FFCP PHASE2:Hg19::chr1:109806865..109806872,+#_40281736166578a191fcacd2e1b6f2a3p10@CELSR2
2.21e-40FFCP PHASE2:Hg19::chr10:1246202..1246207,-#_881117f3d03a5e7eba96cfe2186a09e6p19@ADARB2
2.21e-40FFCP PHASE1:Hg19::chr10:1246202..1246207,-#_881117f3d03a5e7eba96cfe2186a09e6p19@ADARB2
2.21e-40FFCP PHASE2:Hg19::chr9:19513297..19513309,-#_881117f3d03a5e7eba96cfe2186a09e6p4@SLC24A2
2.21e-40FFCP PHASE2:Hg19::chr10:1246245..1246252,-#_881117f3d03a5e7eba96cfe2186a09e6p20@ADARB2
2.21e-40FFCP PHASE1:Hg19::chr10:1246245..1246252,-#_881117f3d03a5e7eba96cfe2186a09e6p20@ADARB2
2.21e-40FFCP PHASE1:Hg19::chr8:27522642..27522647,+#_881117f3d03a5e7eba96cfe2186a09e6p@chr8:27522642..27522647, +










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.