UBERON:0001891
From FANTOM5_SSTAR
| 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: |
| ||
| 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)
- 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
| P-value | FFCP | Short description |
|---|---|---|
| 9.37e-99 | FFCP PHASE2:Hg19::chr1:24915966..24915971,+#_4bb36d079a358f3efb467285a481d68f | p5@C1orf130 |
| 9.37e-99 | FFCP PHASE2:Hg19::chr9:139916913..139916917,+#_4bb36d079a358f3efb467285a481d68f | p@chr9:139916913..139916917, + |
| 9.37e-99 | FFCP PHASE1:Hg19::chr10:62149979..62149980,-#_4bb36d079a358f3efb467285a481d68f | p59@ANK3 |
| 9.37e-99 | FFCP PHASE2:Hg19::chr4:56229918..56229919,-#_4bb36d079a358f3efb467285a481d68f | p@chr4:56229918..56229919, - |
| 9.37e-99 | FFCP PHASE1:Hg19::chr1:24915966..24915971,+#_4bb36d079a358f3efb467285a481d68f | p5@C1orf130 |
| 9.37e-99 | FFCP PHASE1:Hg19::chr9:139916913..139916917,+#_4bb36d079a358f3efb467285a481d68f | p@chr9:139916913..139916917, + |
| 9.37e-99 | FFCP PHASE1:Hg19::chr4:56229918..56229919,-#_4bb36d079a358f3efb467285a481d68f | p@chr4:56229918..56229919, - |
| 9.37e-99 | FFCP PHASE2:Hg19::chr10:62149979..62149980,-#_4bb36d079a358f3efb467285a481d68f | p59@ANK3 |
| 9.37e-99 | FFCP PHASE1:Hg19::chr10:68718064..68718067,-#_4bb36d079a358f3efb467285a481d68f | p@chr10:68718064..68718067, - |
| 9.37e-99 | FFCP PHASE2:Hg19::chr10:68718064..68718067,-#_4bb36d079a358f3efb467285a481d68f | p@chr10:68718064..68718067, - |
| 2.55e-98 | FFCP PHASE2:Hg19::chr1:65776926..65776928,+#_1c887a12805d57770e877d86b51bf8d9 | p@chr1:65776926..65776928, + |
| 2.55e-98 | FFCP PHASE1:Hg19::chr18:74702556..74702558,-#_1c887a12805d57770e877d86b51bf8d9 | p@chr18:74702556..74702558, - |
| 2.55e-98 | FFCP PHASE1:Hg19::chr1:65776926..65776928,+#_1c887a12805d57770e877d86b51bf8d9 | p@chr1:65776926..65776928, + |
| 2.55e-98 | FFCP PHASE2:Hg19::chr5:57935348..57935354,-#_1c887a12805d57770e877d86b51bf8d9 | p@chr5:57935348..57935354, - |
| 2.55e-98 | FFCP PHASE1:Hg19::chr5:57935348..57935354,-#_1c887a12805d57770e877d86b51bf8d9 | p@chr5:57935348..57935354, - |
| 2.55e-98 | FFCP PHASE2:Hg19::chr18:74702556..74702558,-#_1c887a12805d57770e877d86b51bf8d9 | p@chr18:74702556..74702558, - |
| 1.23e-66 | FFCP PHASE2:Hg19::chr16:57309513..57309516,-#_3a917a84f9dc9b11b8639df82e9bf914 | p@chr16:57309513..57309516, - |
| 1.23e-66 | FFCP PHASE1:Hg19::chr16:57309513..57309516,-#_3a917a84f9dc9b11b8639df82e9bf914 | p@chr16:57309513..57309516, - |
| 1.23e-66 | FFCP PHASE2:Hg19::chr8:53312058..53312067,-#_3a917a84f9dc9b11b8639df82e9bf914 | p@chr8:53312058..53312067, - |
| 1.23e-66 | FFCP PHASE1:Hg19::chr8:53312058..53312067,-#_3a917a84f9dc9b11b8639df82e9bf914 | p@chr8:53312058..53312067, - |
| 1.23e-66 | FFCP PHASE2:Hg19::chr16:81170013..81170024,-#_3a917a84f9dc9b11b8639df82e9bf914 | p6@PKD1L2 |
| 1.23e-66 | FFCP PHASE1:Hg19::chr10:22967066..22967069,-#_3a917a84f9dc9b11b8639df82e9bf914 | p@chr10:22967066..22967069, - |
| 1.23e-66 | FFCP PHASE2:Hg19::chr10:22967066..22967069,-#_3a917a84f9dc9b11b8639df82e9bf914 | p@chr10:22967066..22967069, - |
| 1.23e-66 | FFCP PHASE1:Hg19::chr16:81170013..81170024,-#_3a917a84f9dc9b11b8639df82e9bf914 | p6@PKD1L2 |
| 2.39e-66 | FFCP PHASE1:Hg19::chr11:7340444..7340448,+#_e883a6df184d15b6421145a949ae13a0 | p@chr11:7340444..7340448, + |
| 2.39e-66 | FFCP PHASE2:Hg19::chr14:95727527..95727529,-#_e883a6df184d15b6421145a949ae13a0 | p@chr14:95727527..95727529, - |
| 2.39e-66 | FFCP PHASE1:Hg19::chr14:95727527..95727529,-#_e883a6df184d15b6421145a949ae13a0 | p@chr14:95727527..95727529, - |
| 2.39e-66 | FFCP PHASE2:Hg19::chr1:44956567..44956571,+#_e883a6df184d15b6421145a949ae13a0 | p@chr1:44956567..44956571, + |
| 2.39e-66 | FFCP PHASE2:Hg19::chr11:7340444..7340448,+#_e883a6df184d15b6421145a949ae13a0 | p@chr11:7340444..7340448, + |
| 2.39e-66 | FFCP PHASE1:Hg19::chr1:44956567..44956571,+#_e883a6df184d15b6421145a949ae13a0 | p@chr1:44956567..44956571, + |
| 4.66e-66 | FFCP PHASE2:Hg19::chr13:34922094..34922105,+#_a923a0027fa79b41f5fb2827c364276c | p@chr13:34922094..34922105, + |
| 4.66e-66 | FFCP PHASE2:Hg19::chr9:79516011..79516022,-#_a923a0027fa79b41f5fb2827c364276c | p@chr9:79516011..79516022, - |
| 4.66e-66 | FFCP PHASE1:Hg19::chr17:29623232..29623241,-#_a923a0027fa79b41f5fb2827c364276c | p8@OMG |
| 4.66e-66 | FFCP PHASE1:Hg19::chr13:34922094..34922105,+#_a923a0027fa79b41f5fb2827c364276c | p@chr13:34922094..34922105, + |
| 4.66e-66 | FFCP PHASE1:Hg19::chr9:79516011..79516022,-#_a923a0027fa79b41f5fb2827c364276c | p@chr9:79516011..79516022, - |
| 4.66e-66 | FFCP PHASE2:Hg19::chr14:105166013..105166017,+#_a923a0027fa79b41f5fb2827c364276c | p@chr14:105166013..105166017, + |
| 4.66e-66 | FFCP PHASE1:Hg19::chr14:105166013..105166017,+#_a923a0027fa79b41f5fb2827c364276c | p@chr14:105166013..105166017, + |
| 4.66e-66 | FFCP PHASE2:Hg19::chr17:29623232..29623241,-#_a923a0027fa79b41f5fb2827c364276c | p8@OMG |
| 4.66e-66 | FFCP PHASE2:Hg19::chr13:43872447..43872452,-#_a923a0027fa79b41f5fb2827c364276c | p@chr13:43872447..43872452, - |
| 4.66e-66 | FFCP PHASE1:Hg19::chr13:43872447..43872452,-#_a923a0027fa79b41f5fb2827c364276c | p@chr13:43872447..43872452, - |
| 1.46e-50 | FFCP PHASE2:Hg19::chr9:108178201..108178203,+#_e92a00d69d3d1c12dbae63f3900bf6fb | p@chr9:108178201..108178203, + |
| 1.46e-50 | FFCP PHASE1:Hg19::chr9:108178201..108178203,+#_e92a00d69d3d1c12dbae63f3900bf6fb | p@chr9:108178201..108178203, + |
| 1.46e-50 | FFCP PHASE2:Hg19::chrX:28627633..28627642,+#_e92a00d69d3d1c12dbae63f3900bf6fb | p@chrX:28627633..28627642, + |
| 1.46e-50 | FFCP PHASE1:Hg19::chrX:28627633..28627642,+#_e92a00d69d3d1c12dbae63f3900bf6fb | p@chrX:28627633..28627642, + |
| 3.99e-50 | FFCP PHASE2:Hg19::chr20:52570026..52570037,-#_08ad9d1d97f2644b4eb609927c9d4c19 | p@chr20:52570026..52570037, - |
| 3.99e-50 | FFCP PHASE1:Hg19::chr6:89803656..89803659,+#_08ad9d1d97f2644b4eb609927c9d4c19 | p@chr6:89803656..89803659, + |
| 3.99e-50 | FFCP PHASE2:Hg19::chr3:50717966..50717971,+#_08ad9d1d97f2644b4eb609927c9d4c19 | p@chr3:50717966..50717971, + |
| 3.99e-50 | FFCP PHASE1:Hg19::chr20:52570026..52570037,-#_08ad9d1d97f2644b4eb609927c9d4c19 | p@chr20:52570026..52570037, - |
| 3.99e-50 | FFCP PHASE2:Hg19::chr6:134626498..134626502,-#_08ad9d1d97f2644b4eb609927c9d4c19 | p@chr6:134626498..134626502, - |
| 3.99e-50 | FFCP PHASE1:Hg19::chr6:134626498..134626502,-#_08ad9d1d97f2644b4eb609927c9d4c19 | p@chr6:134626498..134626502, - |
| 3.99e-50 | FFCP PHASE1:Hg19::chr3:50717966..50717971,+#_08ad9d1d97f2644b4eb609927c9d4c19 | p@chr3:50717966..50717971, + |
| 3.99e-50 | FFCP PHASE2:Hg19::chr6:89803656..89803659,+#_08ad9d1d97f2644b4eb609927c9d4c19 | p@chr6:89803656..89803659, + |
| 6.58e-50 | FFCP PHASE1:Hg19::chr17:3479944..3479947,-#_44bf015a558107f1b76ee1383a5287ed | p@chr17:3479944..3479947, - |
| 6.58e-50 | FFCP PHASE1:Hg19::chr1:161275096..161275109,-#_44bf015a558107f1b76ee1383a5287ed | p@chr1:161275096..161275109, - |
| 6.58e-50 | FFCP PHASE1:Hg19::chr6:163745521..163745530,-#_44bf015a558107f1b76ee1383a5287ed | p2@LOC285796 |
| 6.58e-50 | FFCP PHASE2:Hg19::chr6:151042126..151042135,+#_44bf015a558107f1b76ee1383a5287ed | p21@PLEKHG1 |
| 6.58e-50 | FFCP PHASE1:Hg19::chr22:48980473..48980481,+#_44bf015a558107f1b76ee1383a5287ed | p@chr22:48980473..48980481, + |
| 6.58e-50 | FFCP PHASE1:Hg19::chr9:137240632..137240635,+#_44bf015a558107f1b76ee1383a5287ed | p@chr9:137240632..137240635, + |
| 6.58e-50 | FFCP PHASE2:Hg19::chr1:160009700..160009711,-#_44bf015a558107f1b76ee1383a5287ed | p10@KCNJ10 |
| 6.58e-50 | FFCP PHASE1:Hg19::chr6:151042126..151042135,+#_44bf015a558107f1b76ee1383a5287ed | p21@PLEKHG1 |
| 6.58e-50 | FFCP PHASE2:Hg19::chr18:26665245..26665249,+#_44bf015a558107f1b76ee1383a5287ed | p@chr18:26665245..26665249, + |
| 6.58e-50 | FFCP PHASE2:Hg19::chr9:19515907..19515918,-#_44bf015a558107f1b76ee1383a5287ed | p@chr9:19515907..19515918, - |
| 6.58e-50 | FFCP PHASE1:Hg19::chr1:160009700..160009711,-#_44bf015a558107f1b76ee1383a5287ed | p10@KCNJ10 |
| 6.58e-50 | FFCP PHASE2:Hg19::chr17:70910145..70910148,-#_44bf015a558107f1b76ee1383a5287ed | p@chr17:70910145..70910148, - |
| 6.58e-50 | FFCP PHASE2:Hg19::chr17:3479944..3479947,-#_44bf015a558107f1b76ee1383a5287ed | p@chr17:3479944..3479947, - |
| 6.58e-50 | FFCP PHASE2:Hg19::chr22:48980473..48980481,+#_44bf015a558107f1b76ee1383a5287ed | p@chr22:48980473..48980481, + |
| 6.58e-50 | FFCP PHASE1:Hg19::chr9:19515907..19515918,-#_44bf015a558107f1b76ee1383a5287ed | p@chr9:19515907..19515918, - |
| 6.58e-50 | FFCP PHASE1:Hg19::chr18:26665245..26665249,+#_44bf015a558107f1b76ee1383a5287ed | p@chr18:26665245..26665249, + |
| 6.58e-50 | FFCP PHASE2:Hg19::chr6:163745521..163745530,-#_44bf015a558107f1b76ee1383a5287ed | p2@LOC285796 |
| 6.58e-50 | FFCP PHASE1:Hg19::chr17:70910145..70910148,-#_44bf015a558107f1b76ee1383a5287ed | p@chr17:70910145..70910148, - |
| 6.58e-50 | FFCP PHASE2:Hg19::chr1:161275096..161275109,-#_44bf015a558107f1b76ee1383a5287ed | p@chr1:161275096..161275109, - |
| 6.58e-50 | FFCP PHASE2:Hg19::chr9:137240632..137240635,+#_44bf015a558107f1b76ee1383a5287ed | p@chr9:137240632..137240635, + |
| 2.38e-43 | FFCP PHASE1:Mm9::chr19:40804786..40804795,-#_3838eb3243f02c74b4aa6452bcc4ca2d | p@chr19:40804786..40804795, - |
| 2.38e-43 | FFCP PHASE2:Mm9::chr19:40804786..40804795,-#_3838eb3243f02c74b4aa6452bcc4ca2d | p@chr19:40804786..40804795, - |
| 6.62e-41 | FFCP PHASE2:Hg19::chr4:139891920..139891924,-#_e77f54ed2f3411eebba5b85c38e26037 | p@chr4:139891920..139891924, - |
| 6.62e-41 | FFCP PHASE1:Hg19::chr4:139891920..139891924,-#_e77f54ed2f3411eebba5b85c38e26037 | p@chr4:139891920..139891924, - |
| 6.62e-41 | FFCP PHASE2:Hg19::chr5:60933634..60933637,+#_e77f54ed2f3411eebba5b85c38e26037 | p4@C5orf64 |
| 6.62e-41 | FFCP PHASE1:Hg19::chr5:60933634..60933637,+#_e77f54ed2f3411eebba5b85c38e26037 | p4@C5orf64 |
| 9.91e-41 | FFCP PHASE2:Hg19::chr13:21100208..21100214,+#_30051241114b8a677c0f197c3372a7a2 | p@chr13:21100208..21100214, + |
| 9.91e-41 | FFCP PHASE1:Hg19::chr13:21100208..21100214,+#_30051241114b8a677c0f197c3372a7a2 | p@chr13:21100208..21100214, + |
| 9.91e-41 | FFCP PHASE2:Hg19::chrX:13792462..13792477,-#_30051241114b8a677c0f197c3372a7a2 | p@chrX:13792462..13792477, - |
| 9.91e-41 | FFCP PHASE1:Hg19::chrX:13792462..13792477,-#_30051241114b8a677c0f197c3372a7a2 | p@chrX:13792462..13792477, - |
| 9.91e-41 | FFCP PHASE2:Hg19::chr5:152017019..152017026,+#_30051241114b8a677c0f197c3372a7a2 | p@chr5:152017019..152017026, + |
| 9.91e-41 | FFCP PHASE1:Hg19::chr5:152017019..152017026,+#_30051241114b8a677c0f197c3372a7a2 | p@chr5:152017019..152017026, + |
| 1.48e-40 | FFCP PHASE2:Hg19::chr9:139911084..139911102,-#_40281736166578a191fcacd2e1b6f2a3 | p@chr9:139911084..139911102, - |
| 1.48e-40 | FFCP PHASE1:Hg19::chr1:109806865..109806872,+#_40281736166578a191fcacd2e1b6f2a3 | p10@CELSR2 |
| 1.48e-40 | FFCP PHASE2:Hg19::chr17:71046459..71046462,-#_40281736166578a191fcacd2e1b6f2a3 | p@chr17:71046459..71046462, - |
| 1.48e-40 | FFCP PHASE1:Hg19::chr9:139911084..139911102,-#_40281736166578a191fcacd2e1b6f2a3 | p@chr9:139911084..139911102, - |
| 1.48e-40 | FFCP PHASE2:Hg19::chr2:135170207..135170218,+#_40281736166578a191fcacd2e1b6f2a3 | p@chr2:135170207..135170218, + |
| 1.48e-40 | FFCP PHASE1:Hg19::chr17:71046459..71046462,-#_40281736166578a191fcacd2e1b6f2a3 | p@chr17:71046459..71046462, - |
| 1.48e-40 | FFCP PHASE2:Hg19::chr1:161275238..161275250,-#_40281736166578a191fcacd2e1b6f2a3 | p@chr1:161275238..161275250, - |
| 1.48e-40 | FFCP PHASE1:Hg19::chr1:161275238..161275250,-#_40281736166578a191fcacd2e1b6f2a3 | p@chr1:161275238..161275250, - |
| 1.48e-40 | FFCP PHASE1:Hg19::chr2:135170207..135170218,+#_40281736166578a191fcacd2e1b6f2a3 | p@chr2:135170207..135170218, + |
| 1.48e-40 | FFCP PHASE2:Hg19::chr1:109806865..109806872,+#_40281736166578a191fcacd2e1b6f2a3 | p10@CELSR2 |
| 2.21e-40 | FFCP PHASE1:Hg19::chr9:19513297..19513309,-#_881117f3d03a5e7eba96cfe2186a09e6 | p4@SLC24A2 |
| 2.21e-40 | FFCP PHASE1:Hg19::chr10:1246202..1246207,-#_881117f3d03a5e7eba96cfe2186a09e6 | p19@ADARB2 |
| 2.21e-40 | FFCP PHASE1:Hg19::chr10:1246245..1246252,-#_881117f3d03a5e7eba96cfe2186a09e6 | p20@ADARB2 |
| 2.21e-40 | FFCP PHASE2:Hg19::chr10:1246202..1246207,-#_881117f3d03a5e7eba96cfe2186a09e6 | p19@ADARB2 |
| 2.21e-40 | FFCP PHASE2:Hg19::chr8:27522642..27522647,+#_881117f3d03a5e7eba96cfe2186a09e6 | p@chr8:27522642..27522647, + |
| 2.21e-40 | FFCP PHASE2:Hg19::chrX:103046993..103046994,+#_881117f3d03a5e7eba96cfe2186a09e6 | p@chrX:103046993..103046994, + |
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.
