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{{UBERON
{{UBERON
|id=UBERON:0000349
|alt_id=UBERON:BTO_0000928-FMA_242000
|name=limbic system
|namespace=
|def="A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. including the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia]." [BIRNLEX:Limbic_system, Wikipedia:Limbic_system]
|xref=BTO:0000928;;FMA:242000;;GAID:615;;http://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Brain_limbicsystem.jpg/200px-Brain_limbicsystem.jpg;;MESH:A.08.186.211.577;;OpenCyc:Mx4rwAeba5wpEbGdrcN5Y29ycA;;SCTID:361342009
|is_a=UBERON:0000467;;UBERON:0004121
|synonym=
|comment=obsoletion recommended. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity.
|comment=obsoletion recommended. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity.
|alt_id=UBERON:BTO_0000928-FMA_242000
|disjoint_from=
|union_of=
|created_by=
|created_by=
|obo_creation_date=
|def="A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. including the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia]." [BIRNLEX:Limbic_system, Wikipedia:Limbic_system]
|subset=
|adjacent_to=
|derives_from=
|derives_from=
|develops_from=
|develops_from=
|disjoint_from=
|has_quality=
|has_quality=
|id=UBERON:0000349
|is_a=UBERON:0000477 ;;UBERON:0004121
|is_obsolete=
|located_in=
|located_in=
|name=limbic system
|namespace=FANTOM
|obo_creation_date=
|part_of=UBERON:0001890
|part_of=UBERON:0001890
|preceded_by=
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|subset=
|synonym=
|union_of=
|xref=BTO:0000928;;FMA:242000;;GAID:615;;http://upload.wikimedia.org/wikipedia/commons/5/5c/Brain_limbicsystem.jpg;;http://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Brain_limbicsystem.jpg/200px-Brain_limbicsystem.jpg;;MESH:A.08.186.211.577;;ncithesaurus:Limbic_System;;OpenCyc:Mx4rwAeba5wpEbGdrcN5Y29ycA;;SCTID:361342009
}}
}}

Latest revision as of 17:08, 12 September 2014

Name:limbic system
Namespace:FANTOM
Definition:"A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. including the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia]." [BIRNLEX:Limbic_system, Wikipedia:Limbic_system]
Xrefs:
links:

BTO:0000928
FMA:242000
GAID:615
[1]
[2]
MESH:A.08.186.211.577
ncithesaurus:Limbic_System
OpenCyc:Mx4rwAeba5wpEbGdrcN5Y29ycA

SCTID:361342009
Comments:obsoletion recommended. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity.
Alt_id: UBERON:BTO_0000928-FMA_242000

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:0000477(anatomical cluster),UBERON:0004121(ectoderm-derived structure)
part_of:UBERON:0001890(forebrain)



Children

part of:UBERON:0001876 (amygdala),UBERON:0001882 (nucleus accumbens),UBERON:0001954 (Ammon's horn)

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)

... further results Mouse (Mus musculus)

... further results


Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with UBERON:0000349 (limbic system), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

P-valueFFCPShort description
7.76e-118FFCP PHASE2:Hg19::chr8:54745692..54745698,-#_519290464ac3c304f76003fdfd619da3p11@ATP6V1H
7.76e-118FFCP PHASE1:Hg19::chr8:54745692..54745698,-#_519290464ac3c304f76003fdfd619da3p11@ATP6V1H
6.64e-89FFCP PHASE1:Hg19::chr2:149881275..149881284,+#_eba07a286397dfe879e41cc6b5c8304cp@chr2:149881275..149881284, +
6.64e-89FFCP PHASE2:Hg19::chr2:149881275..149881284,+#_eba07a286397dfe879e41cc6b5c8304cp@chr2:149881275..149881284, +
1.21e-88FFCP PHASE2:Hg19::chr3:71777824..71777833,-#_62f05e300bccfc16e8370ca30116d5b2p28@EIF4E3
1.21e-88FFCP PHASE1:Hg19::chr3:71777824..71777833,-#_62f05e300bccfc16e8370ca30116d5b2p28@EIF4E3
4.86e-82FFCP PHASE1:Hg19::chr3:131756559..131756572,-#_c80a8730960367074940b22cc7cbfe85p7@CPNE4
4.86e-82FFCP PHASE2:Hg19::chr3:131756559..131756572,-#_c80a8730960367074940b22cc7cbfe85p7@CPNE4
5.75e-82FFCP PHASE1:Hg19::chr11:35281834..35281846,-#_51dfd8e2d3d3eca75776253237c8ff8cp@chr11:35281834..35281846, -
5.75e-82FFCP PHASE2:Hg19::chr11:35281834..35281846,-#_51dfd8e2d3d3eca75776253237c8ff8cp@chr11:35281834..35281846, -
1.42e-79FFCP PHASE2:Hg19::chr13:101712292..101712306,-#_454fb4e88c17d44f7709d193626edf1ep@chr13:101712292..101712306, -
1.42e-79FFCP PHASE1:Hg19::chr13:101712292..101712306,-#_454fb4e88c17d44f7709d193626edf1ep@chr13:101712292..101712306, -
1.56e-71FFCP PHASE2:Hg19::chr11:74047383..74047406,-#_c764e3b4bfd05e0a2187f41ac54d055dp@chr11:74047383..74047406, -
1.56e-71FFCP PHASE1:Hg19::chr11:74047383..74047406,-#_c764e3b4bfd05e0a2187f41ac54d055dp@chr11:74047383..74047406, -
2.75e-71FFCP PHASE1:Hg19::chr8:54752406..54752429,-#_dc4dd7232c1e2e3becc370966e6ef940p5@ATP6V1H
2.75e-71FFCP PHASE2:Hg19::chr8:54752406..54752429,-#_dc4dd7232c1e2e3becc370966e6ef940p5@ATP6V1H
1.27e-70FFCP PHASE2:Hg19::chr5:63258078..63258088,-#_43d62fd99830622745ffea870efb0215p6@HTR1A
1.27e-70FFCP PHASE1:Hg19::chr5:63258078..63258088,-#_43d62fd99830622745ffea870efb0215p6@HTR1A
1.14e-63FFCP PHASE2:Hg19::chr2:242815160..242815176,+#_c0ab58c59405c2de3ef5d111dc92d050p@chr2:242815160..242815176, +
1.14e-63FFCP PHASE1:Hg19::chr2:242815160..242815176,+#_c0ab58c59405c2de3ef5d111dc92d050p@chr2:242815160..242815176, +
1.84e-63FFCP PHASE1:Hg19::chr19:19640188..19640201,+#_c634878ce2d3f4faf4f1a8509bb8128ep@chr19:19640188..19640201, +
1.84e-63FFCP PHASE2:Hg19::chr19:19640188..19640201,+#_c634878ce2d3f4faf4f1a8509bb8128ep@chr19:19640188..19640201, +
4.84e-63FFCP PHASE2:Hg19::chr18:11751516..11751523,+#_577ddce323f3b49179e21c2952eb0783p17@GNAL
4.84e-63FFCP PHASE1:Hg19::chr18:11751516..11751523,+#_577ddce323f3b49179e21c2952eb0783p17@GNAL
1.48e-62FFCP PHASE2:Hg19::chr10:116887377..116887393,+#_c113da4d5b01599b1505cf478d85f65dp@chr10:116887377..116887393, +
1.48e-62FFCP PHASE1:Hg19::chr10:116887377..116887393,+#_c113da4d5b01599b1505cf478d85f65dp@chr10:116887377..116887393, +
6.03e-60FFCP PHASE1:Hg19::chr3:12225071..12225084,+#_73abb8280c98a6a72ccea9077837044ap15@SYN2
6.03e-60FFCP PHASE2:Hg19::chr3:12225071..12225084,+#_73abb8280c98a6a72ccea9077837044ap15@SYN2
2.01e-59FFCP PHASE2:Hg19::chr20:9494967..9494972,+#_1355779b98a72b556eaf073772761d37p16@LAMP5
2.01e-59FFCP PHASE1:Hg19::chr15:40582949..40582989,+#_1355779b98a72b556eaf073772761d37p@chr15:40582949..40582989, +
2.01e-59FFCP PHASE1:Hg19::chr20:9494967..9494972,+#_1355779b98a72b556eaf073772761d37p16@LAMP5
2.01e-59FFCP PHASE2:Hg19::chr15:40582949..40582989,+#_1355779b98a72b556eaf073772761d37p@chr15:40582949..40582989, +
3.0e-59FFCP PHASE2:Hg19::chr5:119669146..119669157,-#_7fd784d7470bb5f340b6446d311a26aap2@ENST00000514240
3.0e-59FFCP PHASE1:Hg19::chr5:119669146..119669157,-#_7fd784d7470bb5f340b6446d311a26aap2@ENST00000514240
3.0e-59FFCP PHASE1:Hg19::chr10:106423509..106423521,+#_7fd784d7470bb5f340b6446d311a26aap@chr10:106423509..106423521, +
3.0e-59FFCP PHASE2:Hg19::chr10:106423509..106423521,+#_7fd784d7470bb5f340b6446d311a26aap@chr10:106423509..106423521, +
6.46e-58FFCP PHASE2:Hg19::chr6:33409535..33409539,+#_e6735f7e9f878500d46f53d8d8518ca5p@chr6:33409535..33409539, +
6.46e-58FFCP PHASE1:Hg19::chr6:33409535..33409539,+#_e6735f7e9f878500d46f53d8d8518ca5p@chr6:33409535..33409539, +
4.31e-57FFCP PHASE1:Hg19::chr11:84844026..84844031,-#_0224047a1641ddd6b308c01fdc01833cp42@DLG2
4.31e-57FFCP PHASE2:Hg19::chr11:84844026..84844031,-#_0224047a1641ddd6b308c01fdc01833cp42@DLG2
5.13e-56FFCP PHASE2:Hg19::chr8:89554843..89554848,+#_a01683d241ed68a31c77ee726fd7e049p2@ENST00000518631
5.13e-56FFCP PHASE1:Hg19::chr8:89554843..89554848,+#_a01683d241ed68a31c77ee726fd7e049p2@ENST00000518631
1.01e-55FFCP PHASE1:Hg19::chr15:27112472..27112483,+#_c5556447247bb43505e53e262dcbe0ddp10@GABRA5
1.01e-55FFCP PHASE2:Hg19::chr15:27112472..27112483,+#_c5556447247bb43505e53e262dcbe0ddp10@GABRA5
5.05e-54FFCP PHASE1:Hg19::chr3:17784228..17784233,-#_d4a214daf9e613755cfad176e7e4dee7p9@TBC1D5
5.05e-54FFCP PHASE2:Hg19::chr3:17784228..17784233,-#_d4a214daf9e613755cfad176e7e4dee7p9@TBC1D5
1.58e-53FFCP PHASE1:Hg19::chr12:120159202..120159216,-#_6fb5bb6bba52aa3fa07b617f01c80c53p@chr12:120159202..120159216, -
1.58e-53FFCP PHASE2:Hg19::chr12:120159202..120159216,-#_6fb5bb6bba52aa3fa07b617f01c80c53p@chr12:120159202..120159216, -
2.19e-53FFCP PHASE2:Hg19::chr9:34502907..34502912,-#_008c446864869d37a166b30598556e55p@chr9:34502907..34502912, -
2.19e-53FFCP PHASE1:Hg19::chr9:34502907..34502912,-#_008c446864869d37a166b30598556e55p@chr9:34502907..34502912, -
3.09e-53FFCP PHASE1:Hg19::chr16:19183671..19183690,+#_cc9f2d2f4d0ede237b2b75cd26f3d168p5@SYT17
3.09e-53FFCP PHASE2:Hg19::chr16:19183671..19183690,+#_cc9f2d2f4d0ede237b2b75cd26f3d168p5@SYT17
3.74e-53FFCP PHASE1:Hg19::chr6:1035766..1035777,+#_4ba248df8765603937d95cf198079364p@chr6:1035766..1035777, +
3.74e-53FFCP PHASE2:Hg19::chr6:1035766..1035777,+#_4ba248df8765603937d95cf198079364p@chr6:1035766..1035777, +
3.74e-53FFCP PHASE1:Hg19::chr21:27650975..27651019,-#_4ba248df8765603937d95cf198079364p@chr21:27650975..27651019, -
3.74e-53FFCP PHASE1:Hg19::chr16:49697056..49697066,-#_4ba248df8765603937d95cf198079364p@chr16:49697056..49697066, -
3.74e-53FFCP PHASE2:Hg19::chr16:49697056..49697066,-#_4ba248df8765603937d95cf198079364p@chr16:49697056..49697066, -
3.74e-53FFCP PHASE2:Hg19::chr21:27650975..27651019,-#_4ba248df8765603937d95cf198079364p@chr21:27650975..27651019, -
4.26e-53FFCP PHASE2:Hg19::chr4:46391095..46391114,-#_012a74640d0a4e5e5e312e4bf88c652cp14@GABRA2
4.26e-53FFCP PHASE1:Hg19::chr4:46391095..46391114,-#_012a74640d0a4e5e5e312e4bf88c652cp14@GABRA2
7.27e-53FFCP PHASE1:Hg19::chr6:95445637..95445675,-#_336bdac614df9aa672ac19b19ce9e5a2p@chr6:95445637..95445675, -
7.27e-53FFCP PHASE2:Hg19::chr6:95445637..95445675,-#_336bdac614df9aa672ac19b19ce9e5a2p@chr6:95445637..95445675, -
1.04e-52FFCP PHASE1:Hg19::chrX:63029135..63029150,-#_2342a5cdcf5486d5125181780c466a01p@chrX:63029135..63029150, -
1.04e-52FFCP PHASE2:Hg19::chrX:63029135..63029150,-#_2342a5cdcf5486d5125181780c466a01p@chrX:63029135..63029150, -
1.38e-52FFCP PHASE2:Hg19::chr6:90272488..90272510,+#_00d9b0f23694a4a08e9a8db7ad0ba69dp7@ANKRD6
1.38e-52FFCP PHASE1:Hg19::chr6:90272488..90272510,+#_00d9b0f23694a4a08e9a8db7ad0ba69dp7@ANKRD6
1.15e-51FFCP PHASE2:Hg19::chr1:20813796..20813807,-#_9efd3543e364c34f51d92d5513c5b7f5p@chr1:20813796..20813807, -
1.15e-51FFCP PHASE1:Hg19::chr1:20813796..20813807,-#_9efd3543e364c34f51d92d5513c5b7f5p@chr1:20813796..20813807, -
1.63e-51FFCP PHASE1:Hg19::chr19:49932793..49932820,-#_07063c7e0c20dfb02757e20d5d86c383p@chr19:49932793..49932820, -
1.63e-51FFCP PHASE2:Hg19::chr19:49932793..49932820,-#_07063c7e0c20dfb02757e20d5d86c383p@chr19:49932793..49932820, -
2.3e-51FFCP PHASE1:Hg19::chrX:13789306..13789315,-#_f8a3ec84c08a3d1035e9cc90880d2365p@chrX:13789306..13789315, -
2.3e-51FFCP PHASE2:Hg19::chrX:13789306..13789315,-#_f8a3ec84c08a3d1035e9cc90880d2365p@chrX:13789306..13789315, -
2.73e-51FFCP PHASE1:Hg19::chr11:123525648..123525658,-#_07fc600f8b65b37d79af28ac77380055p19@SCN3B
2.73e-51FFCP PHASE2:Hg19::chr11:123525648..123525658,-#_07fc600f8b65b37d79af28ac77380055p19@SCN3B
3.24e-51FFCP PHASE2:Hg19::chr7:29845734..29845742,+#_162566dbc87d8aad68976b73be84d1e8p16@WIPF3
3.24e-51FFCP PHASE1:Hg19::chr15:87121973..87122016,+#_162566dbc87d8aad68976b73be84d1e8p@chr15:87121973..87122016, +
3.24e-51FFCP PHASE2:Hg19::chr15:87121973..87122016,+#_162566dbc87d8aad68976b73be84d1e8p@chr15:87121973..87122016, +
3.24e-51FFCP PHASE1:Hg19::chr7:29845734..29845742,+#_162566dbc87d8aad68976b73be84d1e8p16@WIPF3
9.81e-51FFCP PHASE2:Hg19::chr15:80695996..80696014,+#_68602b9d5f76850421e30d74b105f63fp@chr15:80695996..80696014, +
9.81e-51FFCP PHASE1:Hg19::chr15:80695996..80696014,+#_68602b9d5f76850421e30d74b105f63fp@chr15:80695996..80696014, +
1.33e-50FFCP PHASE2:Hg19::chr9:13165461..13165485,-#_2ff5594a69f7e11ca544ba2ddf1dbd6ep13@MPDZ
1.33e-50FFCP PHASE2:Hg19::chr2:11810299..11810302,-#_2ff5594a69f7e11ca544ba2ddf1dbd6ep6@NTSR2
1.33e-50FFCP PHASE1:Hg19::chr9:13165461..13165485,-#_2ff5594a69f7e11ca544ba2ddf1dbd6ep13@MPDZ
1.33e-50FFCP PHASE1:Hg19::chr2:11810299..11810302,-#_2ff5594a69f7e11ca544ba2ddf1dbd6ep6@NTSR2
1.63e-50FFCP PHASE2:Hg19::chr10:126694575..126694592,-#_cf67ec4169ad67d684418c572d731007p16@CTBP2
1.63e-50FFCP PHASE1:Hg19::chr10:126694575..126694592,-#_cf67ec4169ad67d684418c572d731007p16@CTBP2
3.0e-50FFCP PHASE2:Hg19::chr17:1028906..1028930,-#_e70a131b77f34aea94ebb0c536b89e48p20@ABR
3.0e-50FFCP PHASE1:Hg19::chr17:1028906..1028930,-#_e70a131b77f34aea94ebb0c536b89e48p20@ABR
4.99e-50FFCP PHASE2:Hg19::chr15:26147599..26147637,+#_164b6e56c98587ae3bc7481e5634989bp1@ENST00000557171
4.99e-50FFCP PHASE1:Hg19::chr15:26147599..26147637,+#_164b6e56c98587ae3bc7481e5634989bp1@ENST00000557171
3.64e-49FFCP PHASE1:Hg19::chr8:89554909..89554920,+#_25264f261076d915a4b1288117a53296p3@ENST00000518631
3.64e-49FFCP PHASE2:Hg19::chr8:89554909..89554920,+#_25264f261076d915a4b1288117a53296p3@ENST00000518631
4.32e-48FFCP PHASE2:Hg19::chr7:94843579..94843594,-#_54e84b5e1be526aaea838497c8e6e9c2p2@ENST00000417881
4.32e-48FFCP PHASE1:Hg19::chr7:94843579..94843594,-#_54e84b5e1be526aaea838497c8e6e9c2p2@ENST00000417881
7.72e-48FFCP PHASE2:Hg19::chr12:49393231..49393242,-#_d13d3f7affa07e9a172eb37a4963318ep3@DDN
7.72e-48FFCP PHASE1:Hg19::chr12:49393231..49393242,-#_d13d3f7affa07e9a172eb37a4963318ep3@DDN
3.27e-47FFCP PHASE1:Hg19::chr19:49941642..49941657,-#_d4ffc6c4ad1c163df317a6aa7f1c8c83p6@SLC17A7
3.27e-47FFCP PHASE2:Hg19::chr19:49941642..49941657,-#_d4ffc6c4ad1c163df317a6aa7f1c8c83p6@SLC17A7
1.98e-46FFCP PHASE2:Hg19::chr5:22754587..22754623,+#_655e208f27e377b5757f043a8603cb2fp@chr5:22754587..22754623, +
1.98e-46FFCP PHASE1:Hg19::chr5:22754587..22754623,+#_655e208f27e377b5757f043a8603cb2fp@chr5:22754587..22754623, +

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