UBERON:0002038: Difference between revisions
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|has_quality= | |has_quality= | ||
|id=UBERON:0002038 | |id=UBERON:0002038 | ||
|is_a=UBERON:0009661;;UBERON: | |is_a=UBERON:0009661 ;;UBERON:0015212 | ||
|is_obsolete= | |is_obsolete= | ||
|located_in= | |located_in= | ||
Revision as of 11:09, 12 September 2014
| 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: |
| ||
| 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 |
Midbraincrosssection.png]
200px-Midbraincrosssection.png]
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: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
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)
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)
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-value | FFCP | Short description |
|---|---|---|
| 9.37e-99 | FFCP PHASE2:Hg19::chr10:62149979..62149980,-#_8bf8ad5281fa90fe23cabacc60f276fd | p59@ANK3 |
| 9.37e-99 | FFCP PHASE2:Hg19::chr1:24915966..24915971,+#_8bf8ad5281fa90fe23cabacc60f276fd | p5@C1orf130 |
| 9.37e-99 | FFCP PHASE2:Hg19::chr10:68718064..68718067,-#_8bf8ad5281fa90fe23cabacc60f276fd | p@chr10:68718064..68718067, - |
| 9.37e-99 | FFCP PHASE2:Hg19::chr9:139916913..139916917,+#_8bf8ad5281fa90fe23cabacc60f276fd | p@chr9:139916913..139916917, + |
| 9.37e-99 | FFCP PHASE1:Hg19::chr1:24915966..24915971,+#_8bf8ad5281fa90fe23cabacc60f276fd | p5@C1orf130 |
| 9.37e-99 | FFCP PHASE1:Hg19::chr10:62149979..62149980,-#_8bf8ad5281fa90fe23cabacc60f276fd | p59@ANK3 |
| 9.37e-99 | FFCP PHASE2:Hg19::chr4:56229918..56229919,-#_8bf8ad5281fa90fe23cabacc60f276fd | p@chr4:56229918..56229919, - |
| 9.37e-99 | FFCP PHASE1:Hg19::chr10:68718064..68718067,-#_8bf8ad5281fa90fe23cabacc60f276fd | p@chr10:68718064..68718067, - |
| 9.37e-99 | FFCP PHASE1:Hg19::chr9:139916913..139916917,+#_8bf8ad5281fa90fe23cabacc60f276fd | p@chr9:139916913..139916917, + |
| 9.37e-99 | FFCP PHASE1:Hg19::chr4:56229918..56229919,-#_8bf8ad5281fa90fe23cabacc60f276fd | p@chr4:56229918..56229919, - |
| 2.55e-98 | FFCP PHASE1:Hg19::chr5:57935348..57935354,-#_1ade7380aee6de13974e63cfa8861c71 | p@chr5:57935348..57935354, - |
| 2.55e-98 | FFCP PHASE2:Hg19::chr1:65776926..65776928,+#_1ade7380aee6de13974e63cfa8861c71 | p@chr1:65776926..65776928, + |
| 2.55e-98 | FFCP PHASE1:Hg19::chr18:74702556..74702558,-#_1ade7380aee6de13974e63cfa8861c71 | p@chr18:74702556..74702558, - |
| 2.55e-98 | FFCP PHASE1:Hg19::chr1:65776926..65776928,+#_1ade7380aee6de13974e63cfa8861c71 | p@chr1:65776926..65776928, + |
| 2.55e-98 | FFCP PHASE2:Hg19::chr5:57935348..57935354,-#_1ade7380aee6de13974e63cfa8861c71 | p@chr5:57935348..57935354, - |
| 2.55e-98 | FFCP PHASE2:Hg19::chr18:74702556..74702558,-#_1ade7380aee6de13974e63cfa8861c71 | p@chr18:74702556..74702558, - |
| 1.23e-66 | FFCP PHASE2:Hg19::chr10:22967066..22967069,-#_b4f4264185f5c275198e50174f16946e | p@chr10:22967066..22967069, - |
| 1.23e-66 | FFCP PHASE2:Hg19::chr16:57309513..57309516,-#_b4f4264185f5c275198e50174f16946e | p@chr16:57309513..57309516, - |
| 1.23e-66 | FFCP PHASE1:Hg19::chr16:57309513..57309516,-#_b4f4264185f5c275198e50174f16946e | p@chr16:57309513..57309516, - |
| 1.23e-66 | FFCP PHASE2:Hg19::chr8:53312058..53312067,-#_b4f4264185f5c275198e50174f16946e | p@chr8:53312058..53312067, - |
| 1.23e-66 | FFCP PHASE2:Hg19::chr16:81170013..81170024,-#_b4f4264185f5c275198e50174f16946e | p6@PKD1L2 |
| 1.23e-66 | FFCP PHASE1:Hg19::chr10:22967066..22967069,-#_b4f4264185f5c275198e50174f16946e | p@chr10:22967066..22967069, - |
| 1.23e-66 | FFCP PHASE1:Hg19::chr8:53312058..53312067,-#_b4f4264185f5c275198e50174f16946e | p@chr8:53312058..53312067, - |
| 1.23e-66 | FFCP PHASE1:Hg19::chr16:81170013..81170024,-#_b4f4264185f5c275198e50174f16946e | p6@PKD1L2 |
| 2.39e-66 | FFCP PHASE1:Hg19::chr11:7340444..7340448,+#_a5a842c83ebebe113472c290e73f47ec | p@chr11:7340444..7340448, + |
| 2.39e-66 | FFCP PHASE2:Hg19::chr14:95727527..95727529,-#_a5a842c83ebebe113472c290e73f47ec | p@chr14:95727527..95727529, - |
| 2.39e-66 | FFCP PHASE1:Hg19::chr14:95727527..95727529,-#_a5a842c83ebebe113472c290e73f47ec | p@chr14:95727527..95727529, - |
| 2.39e-66 | FFCP PHASE2:Hg19::chr1:44956567..44956571,+#_a5a842c83ebebe113472c290e73f47ec | p@chr1:44956567..44956571, + |
| 2.39e-66 | FFCP PHASE1:Hg19::chr1:44956567..44956571,+#_a5a842c83ebebe113472c290e73f47ec | p@chr1:44956567..44956571, + |
| 2.39e-66 | FFCP PHASE2:Hg19::chr11:7340444..7340448,+#_a5a842c83ebebe113472c290e73f47ec | p@chr11:7340444..7340448, + |
| 4.66e-66 | FFCP PHASE1:Hg19::chr13:43872447..43872452,-#_be73b6a77780dbe9972070d55e007dd4 | p@chr13:43872447..43872452, - |
| 4.66e-66 | FFCP PHASE1:Hg19::chr9:79516011..79516022,-#_be73b6a77780dbe9972070d55e007dd4 | p@chr9:79516011..79516022, - |
| 4.66e-66 | FFCP PHASE2:Hg19::chr13:34922094..34922105,+#_be73b6a77780dbe9972070d55e007dd4 | p@chr13:34922094..34922105, + |
| 4.66e-66 | FFCP PHASE2:Hg19::chr9:79516011..79516022,-#_be73b6a77780dbe9972070d55e007dd4 | p@chr9:79516011..79516022, - |
| 4.66e-66 | FFCP PHASE1:Hg19::chr17:29623232..29623241,-#_be73b6a77780dbe9972070d55e007dd4 | p8@OMG |
| 4.66e-66 | FFCP PHASE1:Hg19::chr13:34922094..34922105,+#_be73b6a77780dbe9972070d55e007dd4 | p@chr13:34922094..34922105, + |
| 4.66e-66 | FFCP PHASE2:Hg19::chr14:105166013..105166017,+#_be73b6a77780dbe9972070d55e007dd4 | p@chr14:105166013..105166017, + |
| 4.66e-66 | FFCP PHASE1:Hg19::chr14:105166013..105166017,+#_be73b6a77780dbe9972070d55e007dd4 | p@chr14:105166013..105166017, + |
| 4.66e-66 | FFCP PHASE2:Hg19::chr17:29623232..29623241,-#_be73b6a77780dbe9972070d55e007dd4 | p8@OMG |
| 4.66e-66 | FFCP PHASE2:Hg19::chr13:43872447..43872452,-#_be73b6a77780dbe9972070d55e007dd4 | p@chr13:43872447..43872452, - |
| 1.46e-50 | FFCP PHASE1:Hg19::chrX:28627633..28627642,+#_5d0ae9df1dbee9ac84711e12860c4d57 | p@chrX:28627633..28627642, + |
| 1.46e-50 | FFCP PHASE2:Hg19::chrX:28627633..28627642,+#_5d0ae9df1dbee9ac84711e12860c4d57 | p@chrX:28627633..28627642, + |
| 1.46e-50 | FFCP PHASE1:Hg19::chr9:108178201..108178203,+#_5d0ae9df1dbee9ac84711e12860c4d57 | p@chr9:108178201..108178203, + |
| 1.46e-50 | FFCP PHASE2:Hg19::chr9:108178201..108178203,+#_5d0ae9df1dbee9ac84711e12860c4d57 | p@chr9:108178201..108178203, + |
| 3.99e-50 | FFCP PHASE2:Hg19::chr6:89803656..89803659,+#_db452abc1b27d0a77b16691c64756baa | p@chr6:89803656..89803659, + |
| 3.99e-50 | FFCP PHASE2:Hg19::chr6:134626498..134626502,-#_db452abc1b27d0a77b16691c64756baa | p@chr6:134626498..134626502, - |
| 3.99e-50 | FFCP PHASE1:Hg19::chr6:134626498..134626502,-#_db452abc1b27d0a77b16691c64756baa | p@chr6:134626498..134626502, - |
| 3.99e-50 | FFCP PHASE2:Hg19::chr20:52570026..52570037,-#_db452abc1b27d0a77b16691c64756baa | p@chr20:52570026..52570037, - |
| 3.99e-50 | FFCP PHASE1:Hg19::chr6:89803656..89803659,+#_db452abc1b27d0a77b16691c64756baa | p@chr6:89803656..89803659, + |
| 3.99e-50 | FFCP PHASE1:Hg19::chr20:52570026..52570037,-#_db452abc1b27d0a77b16691c64756baa | p@chr20:52570026..52570037, - |
| 3.99e-50 | FFCP PHASE2:Hg19::chr3:50717966..50717971,+#_db452abc1b27d0a77b16691c64756baa | p@chr3:50717966..50717971, + |
| 3.99e-50 | FFCP PHASE1:Hg19::chr3:50717966..50717971,+#_db452abc1b27d0a77b16691c64756baa | p@chr3:50717966..50717971, + |
| 6.58e-50 | FFCP PHASE2:Hg19::chr9:137240632..137240635,+#_2eb26db73d5892800a3c64976fd4d1da | p@chr9:137240632..137240635, + |
| 6.58e-50 | FFCP PHASE1:Hg19::chr17:3479944..3479947,-#_2eb26db73d5892800a3c64976fd4d1da | p@chr17:3479944..3479947, - |
| 6.58e-50 | FFCP PHASE1:Hg19::chr1:161275096..161275109,-#_2eb26db73d5892800a3c64976fd4d1da | p@chr1:161275096..161275109, - |
| 6.58e-50 | FFCP PHASE1:Hg19::chr9:19515907..19515918,-#_2eb26db73d5892800a3c64976fd4d1da | p@chr9:19515907..19515918, - |
| 6.58e-50 | FFCP PHASE1:Hg19::chr22:48980473..48980481,+#_2eb26db73d5892800a3c64976fd4d1da | p@chr22:48980473..48980481, + |
| 6.58e-50 | FFCP PHASE2:Hg19::chr1:160009700..160009711,-#_2eb26db73d5892800a3c64976fd4d1da | p10@KCNJ10 |
| 6.58e-50 | FFCP PHASE2:Hg19::chr6:163745521..163745530,-#_2eb26db73d5892800a3c64976fd4d1da | p2@LOC285796 |
| 6.58e-50 | FFCP PHASE2:Hg19::chr18:26665245..26665249,+#_2eb26db73d5892800a3c64976fd4d1da | p@chr18:26665245..26665249, + |
| 6.58e-50 | FFCP PHASE2:Hg19::chr9:19515907..19515918,-#_2eb26db73d5892800a3c64976fd4d1da | p@chr9:19515907..19515918, - |
| 6.58e-50 | FFCP PHASE2:Hg19::chr17:3479944..3479947,-#_2eb26db73d5892800a3c64976fd4d1da | p@chr17:3479944..3479947, - |
| 6.58e-50 | FFCP PHASE1:Hg19::chr1:160009700..160009711,-#_2eb26db73d5892800a3c64976fd4d1da | p10@KCNJ10 |
| 6.58e-50 | FFCP PHASE2:Hg19::chr6:151042126..151042135,+#_2eb26db73d5892800a3c64976fd4d1da | p21@PLEKHG1 |
| 6.58e-50 | FFCP PHASE1:Hg19::chr6:163745521..163745530,-#_2eb26db73d5892800a3c64976fd4d1da | p2@LOC285796 |
| 6.58e-50 | FFCP PHASE2:Hg19::chr17:70910145..70910148,-#_2eb26db73d5892800a3c64976fd4d1da | p@chr17:70910145..70910148, - |
| 6.58e-50 | FFCP PHASE1:Hg19::chr9:137240632..137240635,+#_2eb26db73d5892800a3c64976fd4d1da | p@chr9:137240632..137240635, + |
| 6.58e-50 | FFCP PHASE1:Hg19::chr6:151042126..151042135,+#_2eb26db73d5892800a3c64976fd4d1da | p21@PLEKHG1 |
| 6.58e-50 | FFCP PHASE2:Hg19::chr1:161275096..161275109,-#_2eb26db73d5892800a3c64976fd4d1da | p@chr1:161275096..161275109, - |
| 6.58e-50 | FFCP PHASE2:Hg19::chr22:48980473..48980481,+#_2eb26db73d5892800a3c64976fd4d1da | p@chr22:48980473..48980481, + |
| 6.58e-50 | FFCP PHASE1:Hg19::chr18:26665245..26665249,+#_2eb26db73d5892800a3c64976fd4d1da | p@chr18:26665245..26665249, + |
| 6.58e-50 | FFCP PHASE1:Hg19::chr17:70910145..70910148,-#_2eb26db73d5892800a3c64976fd4d1da | p@chr17:70910145..70910148, - |
| 8.97e-44 | FFCP PHASE1:Mm9::chr4:134073493..134073502,-#_76354d87ae91daae9c10bb6504d6e60e | p@chr4:134073493..134073502, - |
| 8.97e-44 | FFCP PHASE2:Mm9::chr4:134073493..134073502,-#_76354d87ae91daae9c10bb6504d6e60e | p@chr4:134073493..134073502, - |
| 6.62e-41 | FFCP PHASE1:Hg19::chr5:60933634..60933637,+#_64f317c82716dcab66b0cb15e4685183 | p4@C5orf64 |
| 6.62e-41 | FFCP PHASE2:Hg19::chr4:139891920..139891924,-#_64f317c82716dcab66b0cb15e4685183 | p@chr4:139891920..139891924, - |
| 6.62e-41 | FFCP PHASE1:Hg19::chr4:139891920..139891924,-#_64f317c82716dcab66b0cb15e4685183 | p@chr4:139891920..139891924, - |
| 6.62e-41 | FFCP PHASE2:Hg19::chr5:60933634..60933637,+#_64f317c82716dcab66b0cb15e4685183 | p4@C5orf64 |
| 9.91e-41 | FFCP PHASE2:Hg19::chr5:152017019..152017026,+#_32f08e25943d6407150b12b37b141b21 | p@chr5:152017019..152017026, + |
| 9.91e-41 | FFCP PHASE1:Hg19::chrX:13792462..13792477,-#_32f08e25943d6407150b12b37b141b21 | p@chrX:13792462..13792477, - |
| 9.91e-41 | FFCP PHASE2:Hg19::chr13:21100208..21100214,+#_32f08e25943d6407150b12b37b141b21 | p@chr13:21100208..21100214, + |
| 9.91e-41 | FFCP PHASE1:Hg19::chr13:21100208..21100214,+#_32f08e25943d6407150b12b37b141b21 | p@chr13:21100208..21100214, + |
| 9.91e-41 | FFCP PHASE1:Hg19::chr5:152017019..152017026,+#_32f08e25943d6407150b12b37b141b21 | p@chr5:152017019..152017026, + |
| 9.91e-41 | FFCP PHASE2:Hg19::chrX:13792462..13792477,-#_32f08e25943d6407150b12b37b141b21 | p@chrX:13792462..13792477, - |
| 1.48e-40 | FFCP PHASE1:Hg19::chr1:109806865..109806872,+#_79605e91ee589b80f8b39808af6355c2 | p10@CELSR2 |
| 1.48e-40 | FFCP PHASE2:Hg19::chr9:139911084..139911102,-#_79605e91ee589b80f8b39808af6355c2 | p@chr9:139911084..139911102, - |
| 1.48e-40 | FFCP PHASE2:Hg19::chr17:71046459..71046462,-#_79605e91ee589b80f8b39808af6355c2 | p@chr17:71046459..71046462, - |
| 1.48e-40 | FFCP PHASE2:Hg19::chr1:161275238..161275250,-#_79605e91ee589b80f8b39808af6355c2 | p@chr1:161275238..161275250, - |
| 1.48e-40 | FFCP PHASE1:Hg19::chr9:139911084..139911102,-#_79605e91ee589b80f8b39808af6355c2 | p@chr9:139911084..139911102, - |
| 1.48e-40 | FFCP PHASE2:Hg19::chr2:135170207..135170218,+#_79605e91ee589b80f8b39808af6355c2 | p@chr2:135170207..135170218, + |
| 1.48e-40 | FFCP PHASE1:Hg19::chr17:71046459..71046462,-#_79605e91ee589b80f8b39808af6355c2 | p@chr17:71046459..71046462, - |
| 1.48e-40 | FFCP PHASE1:Hg19::chr1:161275238..161275250,-#_79605e91ee589b80f8b39808af6355c2 | p@chr1:161275238..161275250, - |
| 1.48e-40 | FFCP PHASE1:Hg19::chr2:135170207..135170218,+#_79605e91ee589b80f8b39808af6355c2 | p@chr2:135170207..135170218, + |
| 1.48e-40 | FFCP PHASE2:Hg19::chr1:109806865..109806872,+#_79605e91ee589b80f8b39808af6355c2 | p10@CELSR2 |
| 2.21e-40 | FFCP PHASE2:Hg19::chr9:19513297..19513309,-#_eb9b7c007f8dd62d08c1bdd04418f531 | p4@SLC24A2 |
| 2.21e-40 | FFCP PHASE1:Hg19::chrX:103046993..103046994,+#_eb9b7c007f8dd62d08c1bdd04418f531 | p@chrX:103046993..103046994, + |
| 2.21e-40 | FFCP PHASE1:Hg19::chr8:27522642..27522647,+#_eb9b7c007f8dd62d08c1bdd04418f531 | p@chr8:27522642..27522647, + |
| 2.21e-40 | FFCP PHASE1:Hg19::chr10:1246202..1246207,-#_eb9b7c007f8dd62d08c1bdd04418f531 | p19@ADARB2 |
| 2.21e-40 | FFCP PHASE1:Hg19::chr9:19513297..19513309,-#_eb9b7c007f8dd62d08c1bdd04418f531 | p4@SLC24A2 |
| 2.21e-40 | FFCP PHASE1:Hg19::chr10:1246245..1246252,-#_eb9b7c007f8dd62d08c1bdd04418f531 | p20@ADARB2 |
