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{{UBERON
{{UBERON
|id=UBERON:0002038
|alt_id=UBERON:FMA_67947-MA_0000210
|name=substantia nigra
|anatomical_img_id=FMA:67947
|namespace=
|def="Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA]." [FMA:67947, Wikipedia:Substantia_nigra]
|xref=BTO:0000143;;EFO:0000922;;EHDAA2:0004711;;EV:0100247;;FMA:67947;;GAID:581;;http://upload.wikimedia.org/wikipedia/commons/5/5f/Midbraincrosssection.png;;http://upload.wikimedia.org/wikipedia/commons/thumb/5/5f/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
|is_a=UBERON:0009661;;UBERON:0009663
|synonym="nucleus of basis pedunculi" EXACT [];;"Soemmering's substance" EXACT [];;"substancia nigra" RELATED [Wikipedia:Substantia_nigra]
|comment=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
|comment=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
|disjoint_from=
|union_of=
|created_by=
|created_by=
|obo_creation_date=
|def="Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA]." [FMA:67947, Wikipedia:Substantia_nigra]
|subset=uberon_slim
|derives_from=
|derives_from=
|develops_from=
|develops_from=
|disjoint_from=
|has_quality=
|has_quality=
|id=UBERON:0002038
|is_a=UBERON:0009661;;UBERON:0009663
|is_obsolete=
|located_in=
|located_in=
|name=substantia nigra
|namespace=
|obo_creation_date=
|part_of=UBERON:0001891;;UBERON:0002420
|part_of=UBERON:0001891;;UBERON:0002420
|preceded_by=
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/cl-to-uberon.owl;;IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/cl-to-uberon.owl;;IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|is_obsolete=
|subset=uberon_slim
|preceded_by=
|synonym="nucleus of basis pedunculi" EXACT [];;"Soemmering's substance" EXACT [];;"substancia nigra" RELATED [Wikipedia:Substantia_nigra]
|union_of=
|xref=BTO:0000143;;EFO:0000922;;EHDAA2:0004711;;EV:0100247;;FMA:67947;;GAID:581;;http://upload.wikimedia.org/wikipedia/commons/5/5f/Midbraincrosssection.png;;http://upload.wikimedia.org/wikipedia/commons/thumb/5/5f/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
}}
}}

Revision as of 18:41, 29 November 2012

Name:substantia nigra
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<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:0009661(midbrain nucleus),UBERON:0009663(telencephalic nucleus)
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

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:0002038 (substantia nigra), 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::chr10:68718064..68718067,-#_8bf8ad5281fa90fe23cabacc60f276fdp@chr10:68718064..68718067, -
9.37e-99FFCP PHASE2:Hg19::chr4:56229918..56229919,-#_8bf8ad5281fa90fe23cabacc60f276fdp@chr4:56229918..56229919, -
9.37e-99FFCP PHASE1:Hg19::chr1:24915966..24915971,+#_8bf8ad5281fa90fe23cabacc60f276fdp5@C1orf130
9.37e-99FFCP PHASE2:Hg19::chr10:62149979..62149980,-#_8bf8ad5281fa90fe23cabacc60f276fdp59@ANK3
9.37e-99FFCP PHASE1:Hg19::chr9:139916913..139916917,+#_8bf8ad5281fa90fe23cabacc60f276fdp@chr9:139916913..139916917, +
9.37e-99FFCP PHASE2:Hg19::chr1:24915966..24915971,+#_8bf8ad5281fa90fe23cabacc60f276fdp5@C1orf130
9.37e-99FFCP PHASE1:Hg19::chr10:62149979..62149980,-#_8bf8ad5281fa90fe23cabacc60f276fdp59@ANK3
9.37e-99FFCP PHASE2:Hg19::chr10:68718064..68718067,-#_8bf8ad5281fa90fe23cabacc60f276fdp@chr10:68718064..68718067, -
9.37e-99FFCP PHASE1:Hg19::chr4:56229918..56229919,-#_8bf8ad5281fa90fe23cabacc60f276fdp@chr4:56229918..56229919, -
9.37e-99FFCP PHASE2:Hg19::chr9:139916913..139916917,+#_8bf8ad5281fa90fe23cabacc60f276fdp@chr9:139916913..139916917, +
2.55e-98FFCP PHASE1:Hg19::chr18:74702556..74702558,-#_1ade7380aee6de13974e63cfa8861c71p@chr18:74702556..74702558, -
2.55e-98FFCP PHASE1:Hg19::chr1:65776926..65776928,+#_1ade7380aee6de13974e63cfa8861c71p@chr1:65776926..65776928, +
2.55e-98FFCP PHASE2:Hg19::chr5:57935348..57935354,-#_1ade7380aee6de13974e63cfa8861c71p@chr5:57935348..57935354, -
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 PHASE1:Hg19::chr5:57935348..57935354,-#_1ade7380aee6de13974e63cfa8861c71p@chr5:57935348..57935354, -
1.23e-66FFCP PHASE1:Hg19::chr10:22967066..22967069,-#_b4f4264185f5c275198e50174f16946ep@chr10:22967066..22967069, -
1.23e-66FFCP PHASE2: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 PHASE1:Hg19::chr8:53312058..53312067,-#_b4f4264185f5c275198e50174f16946ep@chr8:53312058..53312067, -
1.23e-66FFCP PHASE1:Hg19::chr16:81170013..81170024,-#_b4f4264185f5c275198e50174f16946ep6@PKD1L2
1.23e-66FFCP PHASE2:Hg19::chr16:81170013..81170024,-#_b4f4264185f5c275198e50174f16946ep6@PKD1L2
1.23e-66FFCP PHASE1:Hg19::chr16:57309513..57309516,-#_b4f4264185f5c275198e50174f16946ep@chr16:57309513..57309516, -
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::chr11:7340444..7340448,+#_a5a842c83ebebe113472c290e73f47ecp@chr11:7340444..7340448, +
2.39e-66FFCP PHASE1:Hg19::chr1:44956567..44956571,+#_a5a842c83ebebe113472c290e73f47ecp@chr1:44956567..44956571, +
2.39e-66FFCP PHASE2:Hg19::chr14:95727527..95727529,-#_a5a842c83ebebe113472c290e73f47ecp@chr14:95727527..95727529, -
2.39e-66FFCP PHASE2:Hg19::chr1:44956567..44956571,+#_a5a842c83ebebe113472c290e73f47ecp@chr1:44956567..44956571, +
4.66e-66FFCP PHASE2:Hg19::chr14:105166013..105166017,+#_be73b6a77780dbe9972070d55e007dd4p@chr14:105166013..105166017, +
4.66e-66FFCP PHASE2:Hg19::chr17:29623232..29623241,-#_be73b6a77780dbe9972070d55e007dd4p8@OMG
4.66e-66FFCP PHASE2:Hg19::chr13:43872447..43872452,-#_be73b6a77780dbe9972070d55e007dd4p@chr13:43872447..43872452, -
4.66e-66FFCP PHASE1:Hg19::chr17:29623232..29623241,-#_be73b6a77780dbe9972070d55e007dd4p8@OMG
4.66e-66FFCP PHASE1:Hg19::chr13:34922094..34922105,+#_be73b6a77780dbe9972070d55e007dd4p@chr13:34922094..34922105, +
4.66e-66FFCP PHASE1:Hg19::chr14:105166013..105166017,+#_be73b6a77780dbe9972070d55e007dd4p@chr14:105166013..105166017, +
4.66e-66FFCP PHASE2:Hg19::chr13:34922094..34922105,+#_be73b6a77780dbe9972070d55e007dd4p@chr13:34922094..34922105, +
4.66e-66FFCP PHASE1:Hg19::chr13:43872447..43872452,-#_be73b6a77780dbe9972070d55e007dd4p@chr13:43872447..43872452, -
4.66e-66FFCP PHASE2:Hg19::chr9:79516011..79516022,-#_be73b6a77780dbe9972070d55e007dd4p@chr9:79516011..79516022, -
4.66e-66FFCP PHASE1:Hg19::chr9:79516011..79516022,-#_be73b6a77780dbe9972070d55e007dd4p@chr9:79516011..79516022, -
1.46e-50FFCP PHASE2:Hg19::chr9:108178201..108178203,+#_5d0ae9df1dbee9ac84711e12860c4d57p@chr9:108178201..108178203, +
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, +
3.99e-50FFCP PHASE1:Hg19::chr6:134626498..134626502,-#_db452abc1b27d0a77b16691c64756baap@chr6:134626498..134626502, -
3.99e-50FFCP PHASE2:Hg19::chr3:50717966..50717971,+#_db452abc1b27d0a77b16691c64756baap@chr3:50717966..50717971, +
3.99e-50FFCP PHASE1:Hg19::chr6:89803656..89803659,+#_db452abc1b27d0a77b16691c64756baap@chr6:89803656..89803659, +
3.99e-50FFCP PHASE2:Hg19::chr6:89803656..89803659,+#_db452abc1b27d0a77b16691c64756baap@chr6:89803656..89803659, +
3.99e-50FFCP PHASE1:Hg19::chr20:52570026..52570037,-#_db452abc1b27d0a77b16691c64756baap@chr20:52570026..52570037, -
3.99e-50FFCP PHASE2:Hg19::chr6:134626498..134626502,-#_db452abc1b27d0a77b16691c64756baap@chr6:134626498..134626502, -
3.99e-50FFCP PHASE1:Hg19::chr3:50717966..50717971,+#_db452abc1b27d0a77b16691c64756baap@chr3:50717966..50717971, +
3.99e-50FFCP PHASE2:Hg19::chr20:52570026..52570037,-#_db452abc1b27d0a77b16691c64756baap@chr20:52570026..52570037, -
6.58e-50FFCP PHASE2:Hg19::chr1:161275096..161275109,-#_2eb26db73d5892800a3c64976fd4d1dap@chr1:161275096..161275109, -
6.58e-50FFCP PHASE1:Hg19::chr6:163745521..163745530,-#_2eb26db73d5892800a3c64976fd4d1dap2@LOC285796
6.58e-50FFCP PHASE2:Hg19::chr22:48980473..48980481,+#_2eb26db73d5892800a3c64976fd4d1dap@chr22:48980473..48980481, +
6.58e-50FFCP PHASE1:Hg19::chr1:160009700..160009711,-#_2eb26db73d5892800a3c64976fd4d1dap10@KCNJ10
6.58e-50FFCP PHASE1:Hg19::chr9:137240632..137240635,+#_2eb26db73d5892800a3c64976fd4d1dap@chr9:137240632..137240635, +
6.58e-50FFCP PHASE2:Hg19::chr9:137240632..137240635,+#_2eb26db73d5892800a3c64976fd4d1dap@chr9:137240632..137240635, +
6.58e-50FFCP PHASE1:Hg19::chr6:151042126..151042135,+#_2eb26db73d5892800a3c64976fd4d1dap21@PLEKHG1
6.58e-50FFCP PHASE2:Hg19::chr6:163745521..163745530,-#_2eb26db73d5892800a3c64976fd4d1dap2@LOC285796
6.58e-50FFCP PHASE2:Hg19::chr1:160009700..160009711,-#_2eb26db73d5892800a3c64976fd4d1dap10@KCNJ10
6.58e-50FFCP PHASE1:Hg19::chr18:26665245..26665249,+#_2eb26db73d5892800a3c64976fd4d1dap@chr18:26665245..26665249, +
6.58e-50FFCP PHASE2:Hg19::chr18:26665245..26665249,+#_2eb26db73d5892800a3c64976fd4d1dap@chr18:26665245..26665249, +
6.58e-50FFCP PHASE1:Hg19::chr17:70910145..70910148,-#_2eb26db73d5892800a3c64976fd4d1dap@chr17:70910145..70910148, -
6.58e-50FFCP PHASE1:Hg19::chr17:3479944..3479947,-#_2eb26db73d5892800a3c64976fd4d1dap@chr17:3479944..3479947, -
6.58e-50FFCP PHASE2:Hg19::chr9:19515907..19515918,-#_2eb26db73d5892800a3c64976fd4d1dap@chr9:19515907..19515918, -
6.58e-50FFCP PHASE2:Hg19::chr17:3479944..3479947,-#_2eb26db73d5892800a3c64976fd4d1dap@chr17:3479944..3479947, -
6.58e-50FFCP PHASE1:Hg19::chr1:161275096..161275109,-#_2eb26db73d5892800a3c64976fd4d1dap@chr1:161275096..161275109, -
6.58e-50FFCP PHASE1:Hg19::chr9:19515907..19515918,-#_2eb26db73d5892800a3c64976fd4d1dap@chr9:19515907..19515918, -
6.58e-50FFCP PHASE2:Hg19::chr6:151042126..151042135,+#_2eb26db73d5892800a3c64976fd4d1dap21@PLEKHG1
6.58e-50FFCP PHASE1:Hg19::chr22:48980473..48980481,+#_2eb26db73d5892800a3c64976fd4d1dap@chr22:48980473..48980481, +
6.58e-50FFCP PHASE2: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::chr5:60933634..60933637,+#_64f317c82716dcab66b0cb15e4685183p4@C5orf64
6.62e-41FFCP PHASE1:Hg19::chr4:139891920..139891924,-#_64f317c82716dcab66b0cb15e4685183p@chr4:139891920..139891924, -
6.62e-41FFCP PHASE2:Hg19::chr4:139891920..139891924,-#_64f317c82716dcab66b0cb15e4685183p@chr4:139891920..139891924, -
9.91e-41FFCP PHASE1:Hg19::chr13:21100208..21100214,+#_32f08e25943d6407150b12b37b141b21p@chr13:21100208..21100214, +
9.91e-41FFCP PHASE2:Hg19::chrX:13792462..13792477,-#_32f08e25943d6407150b12b37b141b21p@chrX:13792462..13792477, -
9.91e-41FFCP PHASE1:Hg19::chr5:152017019..152017026,+#_32f08e25943d6407150b12b37b141b21p@chr5:152017019..152017026, +
9.91e-41FFCP PHASE2:Hg19::chr5:152017019..152017026,+#_32f08e25943d6407150b12b37b141b21p@chr5:152017019..152017026, +
9.91e-41FFCP PHASE2:Hg19::chr13:21100208..21100214,+#_32f08e25943d6407150b12b37b141b21p@chr13:21100208..21100214, +
9.91e-41FFCP PHASE1:Hg19::chrX:13792462..13792477,-#_32f08e25943d6407150b12b37b141b21p@chrX:13792462..13792477, -
1.48e-40FFCP PHASE2:Hg19::chr2:135170207..135170218,+#_79605e91ee589b80f8b39808af6355c2p@chr2:135170207..135170218, +
1.48e-40FFCP PHASE1:Hg19::chr9:139911084..139911102,-#_79605e91ee589b80f8b39808af6355c2p@chr9:139911084..139911102, -
1.48e-40FFCP PHASE2:Hg19::chr1:109806865..109806872,+#_79605e91ee589b80f8b39808af6355c2p10@CELSR2
1.48e-40FFCP PHASE1:Hg19::chr17:71046459..71046462,-#_79605e91ee589b80f8b39808af6355c2p@chr17:71046459..71046462, -
1.48e-40FFCP PHASE2:Hg19::chr9:139911084..139911102,-#_79605e91ee589b80f8b39808af6355c2p@chr9:139911084..139911102, -
1.48e-40FFCP PHASE1:Hg19::chr1:161275238..161275250,-#_79605e91ee589b80f8b39808af6355c2p@chr1:161275238..161275250, -
1.48e-40FFCP PHASE2:Hg19::chr17:71046459..71046462,-#_79605e91ee589b80f8b39808af6355c2p@chr17:71046459..71046462, -
1.48e-40FFCP PHASE1:Hg19::chr2:135170207..135170218,+#_79605e91ee589b80f8b39808af6355c2p@chr2:135170207..135170218, +
1.48e-40FFCP PHASE1:Hg19::chr1:109806865..109806872,+#_79605e91ee589b80f8b39808af6355c2p10@CELSR2
1.48e-40FFCP PHASE2:Hg19::chr1:161275238..161275250,-#_79605e91ee589b80f8b39808af6355c2p@chr1:161275238..161275250, -
2.21e-40FFCP PHASE2:Hg19::chr8:27522642..27522647,+#_eb9b7c007f8dd62d08c1bdd04418f531p@chr8:27522642..27522647, +
2.21e-40FFCP PHASE1:Hg19::chr8:27522642..27522647,+#_eb9b7c007f8dd62d08c1bdd04418f531p@chr8:27522642..27522647, +
2.21e-40FFCP PHASE2:Hg19::chrX:103046993..103046994,+#_eb9b7c007f8dd62d08c1bdd04418f531p@chrX:103046993..103046994, +
2.21e-40FFCP PHASE2:Hg19::chr10:1246202..1246207,-#_eb9b7c007f8dd62d08c1bdd04418f531p19@ADARB2
2.21e-40FFCP PHASE1:Hg19::chr9:19513297..19513309,-#_eb9b7c007f8dd62d08c1bdd04418f531p4@SLC24A2
2.21e-40FFCP PHASE2:Hg19::chr10:1246245..1246252,-#_eb9b7c007f8dd62d08c1bdd04418f531p20@ADARB2

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