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UBERON:0004684

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Name:raphe nuclei
Namespace:FANTOM
Definition:"Thin plates of cells in and immediately adjacent to the sagittal plane[NIF]. A moderate-size cluster of nuclei found in the brain stem. Their main function is to release serotonin to the rest of the brain. Selective serotonin reuptake inhibitor (SSRI) antidepressants are believed to act in these nuclei, as well as at their targets. The raphe nuclei are traditionally considered to be the medial portion of the reticular formation, and they appear as a ridge of cells in the center and most medial portion of the brain stem." [https://sourceforge.net/tracker/?func
Xrefs:
links:

FMA:84017
[ Gray694.png Gray694.png]
[ 200px-Gray694.png 200px-Gray694.png]
MESH:A.08.186.211.132.659.632
ncithesaurus:Raphe_Nuclei
NIF_GrossAnatomy:nlx_anat_20090205
TAO:0001429

ZFA:0001429
Synonyms: "nuclei raphes" EXACT [FMA:84017, FMA:TA]
"nuclei raphes" RELATED LATIN [Wikipedia:Raphe_nuclei]
"raphe cluster" RELATED [Wikipedia:Raphe_nuclei]
"raphe nuclei" EXACT [NIF_GrossAnatomy:nlx_anat_20090205]
"raphe nuclei" EXACT [FMA:84017]
"raphe nuclei set" EXACT [FMA:84017]
"raphe nucleus" RELATED [ZFA:0001429]
Comments:we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei'
Subset: 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)
part_of:UBERON:0002275(reticular formation)



Children

part of:CL:0002610 (raphe nuclei neuron)

Ontology Tree: Loaded from BioPortal


FF samples
It includes FANTOM5 samples that overlay the Uberon ontology


Mouse (Mus musculus)


Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with UBERON:0004684 (raphe nuclei), sorted by p-values
Analyst: Hideya Kawaji

link to source dataset
human : data
mouse : data


P-valueFFCPShort description
1.58e-86FFCP PHASE1:Mm9::chr9:67832482..67832485,+#_7d70562ba50b57946b6c3da1fe4b42f9p@chr9:67832482..67832485, +
1.58e-86FFCP PHASE2:Mm9::chr9:67832482..67832485,+#_7d70562ba50b57946b6c3da1fe4b42f9p@chr9:67832482..67832485, +
2.21e-65FFCP PHASE2:Mm9::chr11:6372235..6372242,-#_cb204e10d58536ac0efa05d64c94ca5ep1@ENSMUST00000175144
2.21e-65FFCP PHASE1:Mm9::chr11:6372235..6372242,-#_cb204e10d58536ac0efa05d64c94ca5ep1@ENSMUST00000175144
3.65e-65FFCP PHASE2:Mm9::chr6:77194015..77194026,+#_6a9f27ef0f56483eb269b645006e1248p@chr6:77194015..77194026, +
3.65e-65FFCP PHASE1:Mm9::chr6:77194015..77194026,+#_6a9f27ef0f56483eb269b645006e1248p@chr6:77194015..77194026, +
3.28e-58FFCP PHASE2:Mm9::chr2:24918331..24918345,+#_666078436b582e8638bb03d0ecc57b70p@chr2:24918331..24918345, +
3.28e-58FFCP PHASE1:Mm9::chr2:24918331..24918345,+#_666078436b582e8638bb03d0ecc57b70p@chr2:24918331..24918345, +
4.9e-53FFCP PHASE1:Mm9::chr3:88548978..88548990,-#_a7214f7703af678a78780f6f581bbae7p@chr3:88548978..88548990, -
4.9e-53FFCP PHASE2:Mm9::chr3:88548978..88548990,-#_a7214f7703af678a78780f6f581bbae7p@chr3:88548978..88548990, -
7.35e-53FFCP PHASE2:Mm9::chr10:10408741..10408754,-#_f9fd8d37d620434ec5e72834811c8319p@chr10:10408741..10408754, -
7.35e-53FFCP PHASE1:Mm9::chr10:10408741..10408754,-#_f9fd8d37d620434ec5e72834811c8319p@chr10:10408741..10408754, -
1.1e-52FFCP PHASE1:Mm9::chr3:126639582..126639596,-#_500d7e20b8e066e7518dae392040ae1ap@chr3:126639582..126639596, -
1.1e-52FFCP PHASE2:Mm9::chr3:126639582..126639596,-#_500d7e20b8e066e7518dae392040ae1ap@chr3:126639582..126639596, -
1.65e-52FFCP PHASE2:Mm9::chr12:85023868..85023879,+#_7d8fcae546d446a303a68c4bc1756e43p@chr12:85023868..85023879, +
1.65e-52FFCP PHASE2:Mm9::chr4:57254065..57254072,-#_7d8fcae546d446a303a68c4bc1756e43p@chr4:57254065..57254072, -
1.65e-52FFCP PHASE1:Mm9::chr12:85023868..85023879,+#_7d8fcae546d446a303a68c4bc1756e43p@chr12:85023868..85023879, +
1.65e-52FFCP PHASE1:Mm9::chr4:57254065..57254072,-#_7d8fcae546d446a303a68c4bc1756e43p@chr4:57254065..57254072, -
2.47e-52FFCP PHASE2:Mm9::chr1:66486342..66486351,+#_011f5e7eee4e6a3c25ead5e1e6f2045fp@chr1:66486342..66486351, +
2.47e-52FFCP PHASE1:Mm9::chr1:66486342..66486351,+#_011f5e7eee4e6a3c25ead5e1e6f2045fp@chr1:66486342..66486351, +
2.47e-52FFCP PHASE2:Mm9::chr10:6473752..6473760,-#_011f5e7eee4e6a3c25ead5e1e6f2045fp@chr10:6473752..6473760, -
2.47e-52FFCP PHASE2:Mm9::chr7:67121440..67121451,-#_011f5e7eee4e6a3c25ead5e1e6f2045fp@chr7:67121440..67121451, -
2.47e-52FFCP PHASE1:Mm9::chr7:67121440..67121451,-#_011f5e7eee4e6a3c25ead5e1e6f2045fp@chr7:67121440..67121451, -
2.47e-52FFCP PHASE1:Mm9::chr10:6473752..6473760,-#_011f5e7eee4e6a3c25ead5e1e6f2045f-, p@chr10:6473752..6473760
3.69e-52FFCP PHASE2:Mm9::chr4:57253877..57253880,-#_4796d0deeae5e78e1bf66f3aadbbcf94p@chr4:57253877..57253880, -
3.69e-52FFCP PHASE1:Mm9::chr4:57253877..57253880,-#_4796d0deeae5e78e1bf66f3aadbbcf94p@chr4:57253877..57253880, -
3.69e-52FFCP PHASE2:Mm9::chr4:57253865..57253876,-#_4796d0deeae5e78e1bf66f3aadbbcf94p@chr4:57253865..57253876, -
3.69e-52FFCP PHASE1:Mm9::chr4:57253865..57253876,-#_4796d0deeae5e78e1bf66f3aadbbcf94p@chr4:57253865..57253876, -
5.51e-52FFCP PHASE1:Mm9::chr14:66893581..66893589,-#_ab5a1be5b4525248f0d76ac4b7f8852dp@chr14:66893581..66893589, -
5.51e-52FFCP PHASE2:Mm9::chr14:66893581..66893589,-#_ab5a1be5b4525248f0d76ac4b7f8852dp@chr14:66893581..66893589, -
1.18e-44FFCP PHASE2:Mm9::chr4:134073503..134073512,-#_b335753eb3ba5e3d8f8a8eccbd1357e9p@chr4:134073503..134073512, -
1.18e-44FFCP PHASE2:Mm9::chr1:66743268..66743289,+#_b335753eb3ba5e3d8f8a8eccbd1357e9p@chr1:66743268..66743289, +
1.18e-44FFCP PHASE1:Mm9::chr1:66743268..66743289,+#_b335753eb3ba5e3d8f8a8eccbd1357e9p@chr1:66743268..66743289, +
1.18e-44FFCP PHASE1:Mm9::chr4:134073503..134073512,-#_b335753eb3ba5e3d8f8a8eccbd1357e9p@chr4:134073503..134073512, -
2.33e-44FFCP PHASE2:Mm9::chr8:67087900..67087910,-#_29ff4f9b587deda5f58d0e96e6e23762p@chr8:67087900..67087910, -
2.33e-44FFCP PHASE1:Mm9::chr4:57447275..57447280,+#_29ff4f9b587deda5f58d0e96e6e23762p21@Palm2
2.33e-44FFCP PHASE2:Mm9::chr4:57447275..57447280,+#_29ff4f9b587deda5f58d0e96e6e23762p21@Palm2
2.33e-44FFCP PHASE1:Mm9::chr8:67087900..67087910,-#_29ff4f9b587deda5f58d0e96e6e23762p@chr8:67087900..67087910, -
3.27e-44FFCP PHASE1:Mm9::chr10:111706834..111706844,+#_8bb8ba2f113bfcad5b91ba5d4da1b145p@chr10:111706834..111706844, +
3.27e-44FFCP PHASE2:Mm9::chr9:46721556..46721563,+#_8bb8ba2f113bfcad5b91ba5d4da1b145p5@2900052N01Rik
3.27e-44FFCP PHASE2:Mm9::chr10:111706834..111706844,+#_8bb8ba2f113bfcad5b91ba5d4da1b145p@chr10:111706834..111706844, +
3.27e-44FFCP PHASE1:Mm9::chr9:46721556..46721563,+#_8bb8ba2f113bfcad5b91ba5d4da1b145p5@2900052N01Rik
4.58e-44FFCP PHASE2:Mm9::chr10:6473722..6473734,-#_2dbe468c536f74225dcb1a65110c08c5p@chr10:6473722..6473734, -
4.58e-44FFCP PHASE1:Mm9::chr10:6473722..6473734,-#_2dbe468c536f74225dcb1a65110c08c5p@chr10:6473722..6473734, -
8.97e-44FFCP PHASE2:Mm9::chr9:14438679..14438684,-#_9f395b6cfb6c181b09d30ddcfabd3951p@chr9:14438679..14438684, -
8.97e-44FFCP PHASE1:Mm9::chr9:14438679..14438684,-#_9f395b6cfb6c181b09d30ddcfabd3951p@chr9:14438679..14438684, -
1.75e-43FFCP PHASE1:Mm9::chr4:147732971..147732980,-#_98417e96ba657af9eefc630d3371117ep@chr4:147732971..147732980, -
1.75e-43FFCP PHASE2:Mm9::chr4:147732971..147732980,-#_98417e96ba657af9eefc630d3371117ep@chr4:147732971..147732980, -
2.45e-43FFCP PHASE2:Mm9::chr16:43072307..43072322,+#_3d28b1ebb08a6a47504c4053eba88076p@chr16:43072307..43072322, +
2.45e-43FFCP PHASE1:Mm9::chr16:43072307..43072322,+#_3d28b1ebb08a6a47504c4053eba88076p@chr16:43072307..43072322, +
1.7e-39FFCP PHASE1:Mm9::chr10:6482651..6482660,-#_0942180b4968611b45555cf926370a84p@chr10:6482651..6482660, -
1.7e-39FFCP PHASE2:Mm9::chr10:6482651..6482660,-#_0942180b4968611b45555cf926370a84p@chr10:6482651..6482660, -
2.66e-39FFCP PHASE2:Mm9::chr14:13448641..13448660,-#_9bb6b60df21871fcfd160dd4979bac83p@chr14:13448641..13448660, -
2.66e-39FFCP PHASE1:Mm9::chr14:13448641..13448660,-#_9bb6b60df21871fcfd160dd4979bac83p@chr14:13448641..13448660, -
2.66e-39FFCP PHASE2:Mm9::chr2:103659822..103659827,-#_9bb6b60df21871fcfd160dd4979bac83p1@ENSMUST00000118421, p1@ENSMUST00000167989
2.66e-39FFCP PHASE1:Mm9::chr12:110796949..110796955,+#_9bb6b60df21871fcfd160dd4979bac83p@chr12:110796949..110796955, +
2.66e-39FFCP PHASE2:Mm9::chr12:110796949..110796955,+#_9bb6b60df21871fcfd160dd4979bac83p@chr12:110796949..110796955, +
2.66e-39FFCP PHASE1:Mm9::chr2:103659822..103659827,-#_9bb6b60df21871fcfd160dd4979bac83p1@ENSMUST00000118421, p1@ENSMUST00000167989
4.15e-39FFCP PHASE1:Mm9::chr5:135039704..135039724,-#_9b1c8f982f5e8f978c9ff561e0622a66p@chr5:135039704..135039724, -
4.15e-39FFCP PHASE2:Mm9::chr2:90730407..90730420,+#_9b1c8f982f5e8f978c9ff561e0622a66p@chr2:90730407..90730420, +
4.15e-39FFCP PHASE2:Mm9::chr1:155500060..155500061,+#_9b1c8f982f5e8f978c9ff561e0622a66p19@Rgs8
4.15e-39FFCP PHASE1:Mm9::chr16:43072335..43072346,+#_9b1c8f982f5e8f978c9ff561e0622a66p@chr16:43072335..43072346, +
4.15e-39FFCP PHASE1:Mm9::chr1:155500060..155500061,+#_9b1c8f982f5e8f978c9ff561e0622a66p19@Rgs8
4.15e-39FFCP PHASE2:Mm9::chr5:135039704..135039724,-#_9b1c8f982f5e8f978c9ff561e0622a66p@chr5:135039704..135039724, -
4.15e-39FFCP PHASE2:Mm9::chr16:43072335..43072346,+#_9b1c8f982f5e8f978c9ff561e0622a66+, p@chr16:43072335..43072346
4.15e-39FFCP PHASE1:Mm9::chr2:90730407..90730420,+#_9b1c8f982f5e8f978c9ff561e0622a66p@chr2:90730407..90730420, +
1.17e-38FFCP PHASE2:Mm9::chr16:89818560..89818572,-#_0e4d10ee5017aa9449bfff81263f05d7p17@Tiam1
1.17e-38FFCP PHASE1:Mm9::chr10:77867856..77867866,-#_0e4d10ee5017aa9449bfff81263f05d7p@chr10:77867856..77867866, -
1.17e-38FFCP PHASE1:Mm9::chr7:6659121..6659133,-#_0e4d10ee5017aa9449bfff81263f05d7p@chr7:6659121..6659133, -
1.17e-38FFCP PHASE1:Mm9::chr16:89818560..89818572,-#_0e4d10ee5017aa9449bfff81263f05d7p17@Tiam1
1.17e-38FFCP PHASE2:Mm9::chr7:6659121..6659133,-#_0e4d10ee5017aa9449bfff81263f05d7p@chr7:6659121..6659133, -
1.17e-38FFCP PHASE2:Mm9::chr10:77867856..77867866,-#_0e4d10ee5017aa9449bfff81263f05d7p@chr10:77867856..77867866, -
2.09e-38FFCP PHASE2:Mm9::chr6:48398099..48398121,+#_edfefbad1a4de47f95d717a4245ac3afp2@LOC100505089, p2@Sspo
2.09e-38FFCP PHASE1:Mm9::chr6:48398099..48398121,+#_edfefbad1a4de47f95d717a4245ac3afp2@LOC100505089, p2@Sspo
8.86e-38FFCP PHASE1:Mm9::chr4:47004694..47004703,-#_0348d4a80af929214c026393b1907597p8@Gabbr2
8.86e-38FFCP PHASE2:Mm9::chr4:47004694..47004703,-#_0348d4a80af929214c026393b1907597p8@Gabbr2
1.18e-37FFCP PHASE1:Mm9::chr2:177853871..177853888,+#_b5ee9fb3a11df918cc048d34386c4bbbp18@Phactr3
1.18e-37FFCP PHASE2:Mm9::chr2:177853871..177853888,+#_b5ee9fb3a11df918cc048d34386c4bbbp18@Phactr3
2.1e-37FFCP PHASE2:Mm9::chr4:147588847..147588858,-#_5be94447ee2fd7c8e4b3d0490ce092b3p@chr4:147588847..147588858, -
2.1e-37FFCP PHASE1:Mm9::chr4:147588847..147588858,-#_5be94447ee2fd7c8e4b3d0490ce092b3p@chr4:147588847..147588858, -
3.72e-37FFCP PHASE2:Mm9::chr2:70439780..70439819,+#_f786a6293701e2cbce3fc77fb56bc452p@chr2:70439780..70439819, +
3.72e-37FFCP PHASE1:Mm9::chr2:70439780..70439819,+#_f786a6293701e2cbce3fc77fb56bc452p@chr2:70439780..70439819, +
3.67e-34FFCP PHASE2:Mm9::chr11:68505408..68505413,+#_b97dd26b370fd858d7ba11431bba631ap8@Myh10
3.67e-34FFCP PHASE2:Mm9::chr19:40804786..40804795,-#_b97dd26b370fd858d7ba11431bba631ap@chr19:40804786..40804795, -
3.67e-34FFCP PHASE1:Mm9::chr11:68505408..68505413,+#_b97dd26b370fd858d7ba11431bba631ap8@Myh10
3.67e-34FFCP PHASE1:Mm9::chr19:40804786..40804795,-#_b97dd26b370fd858d7ba11431bba631ap@chr19:40804786..40804795, -
4.74e-34FFCP PHASE1:Mm9::chr5:31441248..31441260,-#_063d6bffd3c4e4ec3547bdc1c03ca18ap1@Ucn
4.74e-34FFCP PHASE2:Mm9::chr5:31441248..31441260,-#_063d6bffd3c4e4ec3547bdc1c03ca18ap1@Ucn
4.74e-34FFCP PHASE2:Mm9::chr2:102621960..102621969,+#_063d6bffd3c4e4ec3547bdc1c03ca18ap@chr2:102621960..102621969, +
4.74e-34FFCP PHASE1:Mm9::chr2:102621960..102621969,+#_063d6bffd3c4e4ec3547bdc1c03ca18ap@chr2:102621960..102621969, +
1.31e-33FFCP PHASE1:Mm9::chr14:31438329..31438344,-#_2787e2e2193114d98937a4f70b326260p@chr14:31438329..31438344, -
1.31e-33FFCP PHASE2:Mm9::chr14:31438329..31438344,-#_2787e2e2193114d98937a4f70b326260p@chr14:31438329..31438344, -
1.31e-33FFCP PHASE1:Mm9::chr7:116903722..116903727,-#_2787e2e2193114d98937a4f70b326260p@chr7:116903722..116903727, -
1.31e-33FFCP PHASE2:Mm9::chr15:59373755..59373758,-#_2787e2e2193114d98937a4f70b326260p@chr15:59373755..59373758, -
1.31e-33FFCP PHASE2:Mm9::chr7:116903722..116903727,-#_2787e2e2193114d98937a4f70b326260p@chr7:116903722..116903727, -
1.31e-33FFCP PHASE1:Mm9::chr15:59373755..59373758,-#_2787e2e2193114d98937a4f70b326260p@chr15:59373755..59373758, -
2.18e-33FFCP PHASE1:Mm9::chr14:54813640..54813649,+#_e0524cc8f2ba8eda6272a5a3a078c2d2p@chr14:54813640..54813649, +
2.18e-33FFCP PHASE2:Mm9::chr14:54813640..54813649,+#_e0524cc8f2ba8eda6272a5a3a078c2d2+, p@chr14:54813640..54813649
7.68e-33FFCP PHASE2:Mm9::chr19:55969998..55970001,+#_3a43c380d4d6e3e057d626fb742e9a28p40@Tcf7l2
7.68e-33FFCP PHASE2:Mm9::chr18:62483890..62483902,+#_3a43c380d4d6e3e057d626fb742e9a28p3@Htr4