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UBERON:0002038

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Name:substantia nigra
Namespace:FANTOM
Definition:"Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA]." [FMA:67947, Wikipedia:Substantia_nigra]
Xrefs:
links:

BTO:0000143
EFO:0000922
EHDAA2:0004711
EV:0100247
FMA:67947
GAID:581
[ Midbraincrosssection.png Midbraincrosssection.png]
[ 200px-Midbraincrosssection.png 200px-Midbraincrosssection.png]
MA:0000210
MAT:0000504
MESH:A.08.186.211.132.659.687
ncithesaurus:Substantia_Nigra
NIF_GrossAnatomy:birnlex_789

SCTID:279286002
Synonyms: "nucleus of basis pedunculi" EXACT []
"Soemmering's substance" EXACT []
"substancia nigra" RELATED [Wikipedia:Substantia_nigra]
Comments:TODO: In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA
Alt_id: UBERON:FMA_67947-MA_0000210
Subset: uberon_slim

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:0009661(midbrain nucleus),UBERON:0015212(lateral structure)
part_of:UBERON:0001891(midbrain),UBERON:0002420(basal ganglion)



Children

is a:FF:10358-105E7 (substantia nigra, newborn, donor10223),FF:10371-105G2 (substantia nigra, adult, donor10258)
derives from:FF:0010158 (human substantia nigra - adult donor sample)
part of:CL:0002614 (neuron of the substantia nigra)

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:0002038 (substantia nigra), sorted by p-values
Analyst: Hideya Kawaji

link to source dataset
human : data
mouse : data


P-valueFFCPShort description
9.37e-99FFCP PHASE1:Hg19::chr1:24915966..24915971,+#_8bf8ad5281fa90fe23cabacc60f276fdp5@C1orf130
9.37e-99FFCP PHASE1:Hg19::chr10:62149979..62149980,-#_8bf8ad5281fa90fe23cabacc60f276fdp59@ANK3
9.37e-99FFCP PHASE2:Hg19::chr1:24915966..24915971,+#_8bf8ad5281fa90fe23cabacc60f276fdp5@C1orf130
9.37e-99FFCP PHASE2:Hg19::chr9:139916913..139916917,+#_8bf8ad5281fa90fe23cabacc60f276fd+, p@chr9:139916913..139916917
9.37e-99FFCP PHASE1:Hg19::chr10:68718064..68718067,-#_8bf8ad5281fa90fe23cabacc60f276fdp@chr10:68718064..68718067, -
9.37e-99FFCP PHASE2:Hg19::chr10:68718064..68718067,-#_8bf8ad5281fa90fe23cabacc60f276fdp@chr10:68718064..68718067, -
9.37e-99FFCP PHASE2:Hg19::chr4:56229918..56229919,-#_8bf8ad5281fa90fe23cabacc60f276fdp@chr4:56229918..56229919, -
9.37e-99FFCP PHASE1:Hg19::chr9:139916913..139916917,+#_8bf8ad5281fa90fe23cabacc60f276fdp@chr9:139916913..139916917, +
9.37e-99FFCP PHASE2:Hg19::chr10:62149979..62149980,-#_8bf8ad5281fa90fe23cabacc60f276fdp59@ANK3
9.37e-99FFCP PHASE1:Hg19::chr4:56229918..56229919,-#_8bf8ad5281fa90fe23cabacc60f276fdp@chr4:56229918..56229919, -
2.55e-98FFCP PHASE1:Hg19::chr5:57935348..57935354,-#_1ade7380aee6de13974e63cfa8861c71p@chr5:57935348..57935354, -
2.55e-98FFCP PHASE1:Hg19::chr18:74702556..74702558,-#_1ade7380aee6de13974e63cfa8861c71p@chr18:74702556..74702558, -
2.55e-98FFCP PHASE2:Hg19::chr18:74702556..74702558,-#_1ade7380aee6de13974e63cfa8861c71p@chr18:74702556..74702558, -
2.55e-98FFCP PHASE2:Hg19::chr1:65776926..65776928,+#_1ade7380aee6de13974e63cfa8861c71p@chr1:65776926..65776928, +
2.55e-98FFCP PHASE2:Hg19::chr5:57935348..57935354,-#_1ade7380aee6de13974e63cfa8861c71p@chr5:57935348..57935354, -
2.55e-98FFCP PHASE1:Hg19::chr1:65776926..65776928,+#_1ade7380aee6de13974e63cfa8861c71p@chr1:65776926..65776928, +
1.23e-66FFCP PHASE1:Hg19::chr16:81170013..81170024,-#_b4f4264185f5c275198e50174f16946ep6@PKD1L2
1.23e-66FFCP PHASE1:Hg19::chr8:53312058..53312067,-#_b4f4264185f5c275198e50174f16946ep@chr8:53312058..53312067, -
1.23e-66FFCP PHASE1:Hg19::chr16:57309513..57309516,-#_b4f4264185f5c275198e50174f16946ep@chr16:57309513..57309516, -
1.23e-66FFCP PHASE1:Hg19::chr10:22967066..22967069,-#_b4f4264185f5c275198e50174f16946ep@chr10:22967066..22967069, -
1.23e-66FFCP PHASE2:Hg19::chr16:57309513..57309516,-#_b4f4264185f5c275198e50174f16946ep@chr16:57309513..57309516, -
1.23e-66FFCP PHASE2:Hg19::chr8:53312058..53312067,-#_b4f4264185f5c275198e50174f16946ep@chr8:53312058..53312067, -
1.23e-66FFCP PHASE2:Hg19::chr16:81170013..81170024,-#_b4f4264185f5c275198e50174f16946ep6@PKD1L2
1.23e-66FFCP PHASE2:Hg19::chr10:22967066..22967069,-#_b4f4264185f5c275198e50174f16946ep@chr10:22967066..22967069, -
2.39e-66FFCP PHASE2:Hg19::chr14:95727527..95727529,-#_a5a842c83ebebe113472c290e73f47ecp@chr14:95727527..95727529, -
2.39e-66FFCP PHASE1:Hg19::chr1:44956567..44956571,+#_a5a842c83ebebe113472c290e73f47ecp@chr1:44956567..44956571, +
2.39e-66FFCP PHASE1:Hg19::chr14:95727527..95727529,-#_a5a842c83ebebe113472c290e73f47ecp@chr14:95727527..95727529, -
2.39e-66FFCP PHASE1:Hg19::chr11:7340444..7340448,+#_a5a842c83ebebe113472c290e73f47ecp@chr11:7340444..7340448, +
2.39e-66FFCP PHASE2:Hg19::chr1:44956567..44956571,+#_a5a842c83ebebe113472c290e73f47ecp@chr1:44956567..44956571, +
2.39e-66FFCP PHASE2:Hg19::chr11:7340444..7340448,+#_a5a842c83ebebe113472c290e73f47ecp@chr11:7340444..7340448, +
4.66e-66FFCP PHASE1:Hg19::chr14:105166013..105166017,+#_be73b6a77780dbe9972070d55e007dd4p@chr14:105166013..105166017, +
4.66e-66FFCP PHASE1:Hg19::chr13:43872447..43872452,-#_be73b6a77780dbe9972070d55e007dd4p@chr13:43872447..43872452, -
4.66e-66FFCP PHASE2:Hg19::chr13:34922094..34922105,+#_be73b6a77780dbe9972070d55e007dd4p@chr13:34922094..34922105, +
4.66e-66FFCP PHASE1:Hg19::chr17:29623232..29623241,-#_be73b6a77780dbe9972070d55e007dd4p8@OMG
4.66e-66FFCP PHASE2:Hg19::chr17:29623232..29623241,-#_be73b6a77780dbe9972070d55e007dd4p8@OMG
4.66e-66FFCP PHASE1:Hg19::chr9:79516011..79516022,-#_be73b6a77780dbe9972070d55e007dd4p@chr9:79516011..79516022, -
4.66e-66FFCP PHASE1:Hg19::chr13:34922094..34922105,+#_be73b6a77780dbe9972070d55e007dd4p@chr13:34922094..34922105, +
4.66e-66FFCP PHASE2:Hg19::chr14:105166013..105166017,+#_be73b6a77780dbe9972070d55e007dd4p@chr14:105166013..105166017, +
4.66e-66FFCP PHASE2:Hg19::chr9:79516011..79516022,-#_be73b6a77780dbe9972070d55e007dd4p@chr9:79516011..79516022, -
4.66e-66FFCP PHASE2:Hg19::chr13:43872447..43872452,-#_be73b6a77780dbe9972070d55e007dd4p@chr13:43872447..43872452, -
1.46e-50FFCP PHASE1:Hg19::chr9:108178201..108178203,+#_5d0ae9df1dbee9ac84711e12860c4d57p@chr9:108178201..108178203, +
1.46e-50FFCP PHASE2:Hg19::chrX:28627633..28627642,+#_5d0ae9df1dbee9ac84711e12860c4d57p@chrX:28627633..28627642, +
1.46e-50FFCP PHASE1:Hg19::chrX:28627633..28627642,+#_5d0ae9df1dbee9ac84711e12860c4d57p@chrX:28627633..28627642, +
1.46e-50FFCP PHASE2:Hg19::chr9:108178201..108178203,+#_5d0ae9df1dbee9ac84711e12860c4d57p@chr9:108178201..108178203, +
3.99e-50FFCP PHASE1:Hg19::chr3:50717966..50717971,+#_db452abc1b27d0a77b16691c64756baa+, p@chr3:50717966..50717971
3.99e-50FFCP PHASE1:Hg19::chr20:52570026..52570037,-#_db452abc1b27d0a77b16691c64756baap@chr20:52570026..52570037, -
3.99e-50FFCP PHASE1:Hg19::chr6:134626498..134626502,-#_db452abc1b27d0a77b16691c64756baap@chr6:134626498..134626502, -
3.99e-50FFCP PHASE1:Hg19::chr6:89803656..89803659,+#_db452abc1b27d0a77b16691c64756baap@chr6:89803656..89803659, +
3.99e-50FFCP PHASE2:Hg19::chr20:52570026..52570037,-#_db452abc1b27d0a77b16691c64756baap@chr20:52570026..52570037, -
3.99e-50FFCP PHASE2:Hg19::chr6:134626498..134626502,-#_db452abc1b27d0a77b16691c64756baap@chr6:134626498..134626502, -
3.99e-50FFCP PHASE2:Hg19::chr3:50717966..50717971,+#_db452abc1b27d0a77b16691c64756baap@chr3:50717966..50717971, +
3.99e-50FFCP PHASE2:Hg19::chr6:89803656..89803659,+#_db452abc1b27d0a77b16691c64756baap@chr6:89803656..89803659, +
6.58e-50FFCP PHASE2:Hg19::chr1:160009700..160009711,-#_2eb26db73d5892800a3c64976fd4d1dap10@KCNJ10
6.58e-50FFCP PHASE1:Hg19::chr17:3479944..3479947,-#_2eb26db73d5892800a3c64976fd4d1dap@chr17:3479944..3479947, -
6.58e-50FFCP PHASE1:Hg19::chr9:137240632..137240635,+#_2eb26db73d5892800a3c64976fd4d1dap@chr9:137240632..137240635, +
6.58e-50FFCP PHASE1:Hg19::chr1:160009700..160009711,-#_2eb26db73d5892800a3c64976fd4d1dap10@KCNJ10
6.58e-50FFCP PHASE2:Hg19::chr9:137240632..137240635,+#_2eb26db73d5892800a3c64976fd4d1dap@chr9:137240632..137240635, +
6.58e-50FFCP PHASE1:Hg19::chr6:163745521..163745530,-#_2eb26db73d5892800a3c64976fd4d1dap2@LOC285796
6.58e-50FFCP PHASE2:Hg19::chr6:151042126..151042135,+#_2eb26db73d5892800a3c64976fd4d1dap21@PLEKHG1
6.58e-50FFCP PHASE1:Hg19::chr9:19515907..19515918,-#_2eb26db73d5892800a3c64976fd4d1dap@chr9:19515907..19515918, -
6.58e-50FFCP PHASE2:Hg19::chr17:3479944..3479947,-#_2eb26db73d5892800a3c64976fd4d1da-, p@chr17:3479944..3479947
6.58e-50FFCP PHASE2:Hg19::chr22:48980473..48980481,+#_2eb26db73d5892800a3c64976fd4d1dap@chr22:48980473..48980481, +
6.58e-50FFCP PHASE1:Hg19::chr22:48980473..48980481,+#_2eb26db73d5892800a3c64976fd4d1dap@chr22:48980473..48980481, +
6.58e-50FFCP PHASE1:Hg19::chr6:151042126..151042135,+#_2eb26db73d5892800a3c64976fd4d1dap21@PLEKHG1
6.58e-50FFCP PHASE2:Hg19::chr18:26665245..26665249,+#_2eb26db73d5892800a3c64976fd4d1dap@chr18:26665245..26665249, +
6.58e-50FFCP PHASE2:Hg19::chr17:70910145..70910148,-#_2eb26db73d5892800a3c64976fd4d1dap@chr17:70910145..70910148, -
6.58e-50FFCP PHASE1:Hg19::chr1:161275096..161275109,-#_2eb26db73d5892800a3c64976fd4d1dap@chr1:161275096..161275109, -
6.58e-50FFCP PHASE1:Hg19::chr18:26665245..26665249,+#_2eb26db73d5892800a3c64976fd4d1dap@chr18:26665245..26665249, +
6.58e-50FFCP PHASE2:Hg19::chr1:161275096..161275109,-#_2eb26db73d5892800a3c64976fd4d1da-, p@chr1:161275096..161275109
6.58e-50FFCP PHASE2:Hg19::chr6:163745521..163745530,-#_2eb26db73d5892800a3c64976fd4d1dap2@LOC285796
6.58e-50FFCP PHASE2:Hg19::chr9:19515907..19515918,-#_2eb26db73d5892800a3c64976fd4d1dap@chr9:19515907..19515918, -
6.58e-50FFCP PHASE1:Hg19::chr17:70910145..70910148,-#_2eb26db73d5892800a3c64976fd4d1dap@chr17:70910145..70910148, -
8.97e-44FFCP PHASE2:Mm9::chr4:134073493..134073502,-#_76354d87ae91daae9c10bb6504d6e60ep@chr4:134073493..134073502, -
8.97e-44FFCP PHASE1:Mm9::chr4:134073493..134073502,-#_76354d87ae91daae9c10bb6504d6e60ep@chr4:134073493..134073502, -
6.62e-41FFCP PHASE1:Hg19::chr5:60933634..60933637,+#_64f317c82716dcab66b0cb15e4685183p4@C5orf64
6.62e-41FFCP PHASE2:Hg19::chr4:139891920..139891924,-#_64f317c82716dcab66b0cb15e4685183p@chr4:139891920..139891924, -
6.62e-41FFCP PHASE2:Hg19::chr5:60933634..60933637,+#_64f317c82716dcab66b0cb15e4685183p4@C5orf64
6.62e-41FFCP PHASE1:Hg19::chr4:139891920..139891924,-#_64f317c82716dcab66b0cb15e4685183p@chr4:139891920..139891924, -
9.91e-41FFCP PHASE2:Hg19::chr13:21100208..21100214,+#_32f08e25943d6407150b12b37b141b21p@chr13:21100208..21100214, +
9.91e-41FFCP PHASE1:Hg19::chr5:152017019..152017026,+#_32f08e25943d6407150b12b37b141b21p@chr5:152017019..152017026, +
9.91e-41FFCP PHASE2:Hg19::chrX:13792462..13792477,-#_32f08e25943d6407150b12b37b141b21p@chrX:13792462..13792477, -
9.91e-41FFCP PHASE1:Hg19::chrX:13792462..13792477,-#_32f08e25943d6407150b12b37b141b21p@chrX:13792462..13792477, -
9.91e-41FFCP PHASE1:Hg19::chr13:21100208..21100214,+#_32f08e25943d6407150b12b37b141b21p@chr13:21100208..21100214, +
9.91e-41FFCP PHASE2:Hg19::chr5:152017019..152017026,+#_32f08e25943d6407150b12b37b141b21p@chr5:152017019..152017026, +
1.48e-40FFCP PHASE1:Hg19::chr2:135170207..135170218,+#_79605e91ee589b80f8b39808af6355c2p@chr2:135170207..135170218, +
1.48e-40FFCP PHASE2:Hg19::chr17:71046459..71046462,-#_79605e91ee589b80f8b39808af6355c2p@chr17:71046459..71046462, -
1.48e-40FFCP PHASE2:Hg19::chr1:109806865..109806872,+#_79605e91ee589b80f8b39808af6355c2p10@CELSR2
1.48e-40FFCP PHASE1:Hg19::chr1:161275238..161275250,-#_79605e91ee589b80f8b39808af6355c2p@chr1:161275238..161275250, -
1.48e-40FFCP PHASE2:Hg19::chr2:135170207..135170218,+#_79605e91ee589b80f8b39808af6355c2p@chr2:135170207..135170218, +
1.48e-40FFCP PHASE2:Hg19::chr1:161275238..161275250,-#_79605e91ee589b80f8b39808af6355c2p@chr1:161275238..161275250, -
1.48e-40FFCP PHASE1:Hg19::chr17:71046459..71046462,-#_79605e91ee589b80f8b39808af6355c2p@chr17:71046459..71046462, -
1.48e-40FFCP PHASE2:Hg19::chr9:139911084..139911102,-#_79605e91ee589b80f8b39808af6355c2-, p@chr9:139911084..139911102
1.48e-40FFCP PHASE1:Hg19::chr1:109806865..109806872,+#_79605e91ee589b80f8b39808af6355c2p10@CELSR2
1.48e-40FFCP PHASE1:Hg19::chr9:139911084..139911102,-#_79605e91ee589b80f8b39808af6355c2p@chr9:139911084..139911102, -
2.21e-40FFCP PHASE2:Hg19::chr10:1246202..1246207,-#_eb9b7c007f8dd62d08c1bdd04418f531p19@ADARB2
2.21e-40FFCP PHASE1:Hg19::chr10:1246245..1246252,-#_eb9b7c007f8dd62d08c1bdd04418f531p20@ADARB2
2.21e-40FFCP PHASE1:Hg19::chr8:27522642..27522647,+#_eb9b7c007f8dd62d08c1bdd04418f531p@chr8:27522642..27522647, +
2.21e-40FFCP PHASE2:Hg19::chr10:1246245..1246252,-#_eb9b7c007f8dd62d08c1bdd04418f531p20@ADARB2
2.21e-40FFCP PHASE2:Hg19::chr9:19513297..19513309,-#_eb9b7c007f8dd62d08c1bdd04418f531p4@SLC24A2
2.21e-40FFCP PHASE1:Hg19::chrX:103046993..103046994,+#_eb9b7c007f8dd62d08c1bdd04418f531p@chrX:103046993..103046994, +