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{{UBERON
{{UBERON
|id=UBERON:0002421
|name=hippocampal formation
|namespace=
|def="Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment]." [UBERON:cjm]
|xref=ABA:HPF;;BM:Tel-HF;;BTO:0000601;;FMA:74038;;MA:0000189;;NIF_GrossAnatomy:birnlex_715;;SCTID:422867004
|is_a=UBERON:0002791
|synonym="archipallium" RELATED [MA:0000189];;"hippocampus" NARROW [BTO:0000601, GO:0021766];;"hippocampus (crosby)" EXACT [];;"major hippocampus" RELATED [BTO:0000601];;"primal cortex" RELATED [MA:0000189]
|comment=Usage notes: The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum[NIF]. BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says "hippocampus" it means "hippocampal formation". In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH.
|alt_id=UBERON:MA_0000189-FMA_74038
|alt_id=UBERON:MA_0000189-FMA_74038
|disjoint_from=
|comment=Usage notes: The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum[NIF]. BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says "hippocampus" it means "hippocampal formation". In ABA HPF
|union_of=
|created_by=
|created_by=
|obo_creation_date=
|def="Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment]." [UBERON:cjm]
|subset=uberon_slim
|derives_from=
|derives_from=
|develops_from=
|develops_from=
|disjoint_from=
|has_quality=
|has_quality=
|id=UBERON:0002421
|is_a=UBERON:0002791
|is_obsolete=
|located_in=
|located_in=
|name=hippocampal formation
|namespace=FANTOM
|obo_creation_date=
|part_of=UBERON:0000203
|part_of=UBERON:0000203
|preceded_by=
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl;;"spatially_disjoint_from" UBERON:0001950;;"spatially_disjoint_from" UBERON:0002264
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl;;"spatially_disjoint_from" UBERON:0001950;;"spatially_disjoint_from" UBERON:0002264
|is_obsolete=
|subset=uberon_slim
|preceded_by=
|synonym="archipallium" RELATED [MA:0000189];;"hippocampus" NARROW [BTO:0000601, GO:0021766];;"hippocampus (crosby)" EXACT [];;"major hippocampus" RELATED [BTO:0000601];;"primal cortex" RELATED [MA:0000189]
|union_of=
|xref=ABA:HPF;;BM:Tel-HF;;BTO:0000601;;FMA:74038;;MA:0000189;;NIF_GrossAnatomy:birnlex_715;;SCTID:422867004
}}
}}

Latest revision as of 17:32, 12 September 2014

Name:hippocampal formation
Namespace:FANTOM
Definition:"Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment]." [UBERON:cjm]
Xrefs:
links:

ABA:HPF
BM:Tel-HF
BTO:0000601
FMA:74038
MA:0000189
NIF_GrossAnatomy:birnlex_715

SCTID:422867004
Synonyms: "archipallium" RELATED [MA:0000189]
"hippocampus" NARROW [BTO:0000601, GO:0021766]
"hippocampus (crosby)" EXACT []
"major hippocampus" RELATED [BTO:0000601]
"primal cortex" RELATED [MA:0000189]
Comments:Usage notes: The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum[NIF]. BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says "hippocampus" it means "hippocampal formation". In ABA HPF
Alt_id: UBERON:MA_0000189-FMA_74038
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:0002791(regional part of telencephalon)
part_of:UBERON:0000203(pallium)



Children

part of:FF:0000197 (mouse astrocyte of hippocampus sample),UBERON:0001954 (Ammon's horn),FF:0010153 (hippocampus - adult sample),FF:0011391 (mouse hippocampus- neonate N00 sample),FF:13-16E8 (hippocampus, adult),FF:627-43G1 (hippocampus, neonate N00)

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:0002421 (hippocampal formation), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

P-valueFFCPShort description
5.68e-99FFCP PHASE2:Hg19::chrX:148561320..148561329,-#_34ef90ebb24c287e0129720e4bcc043bp@chrX:148561320..148561329, -
5.68e-99FFCP PHASE1:Hg19::chr2:149881275..149881284,+#_34ef90ebb24c287e0129720e4bcc043bp@chr2:149881275..149881284, +
5.68e-99FFCP PHASE1:Hg19::chrX:148561320..148561329,-#_34ef90ebb24c287e0129720e4bcc043bp@chrX:148561320..148561329, -
5.68e-99FFCP PHASE2:Hg19::chr2:149881275..149881284,+#_34ef90ebb24c287e0129720e4bcc043bp@chr2:149881275..149881284, +
1.55e-98FFCP PHASE2:Hg19::chr2:187628574..187628585,+#_c444c6931f327308e73295794586b2b1p@chr2:187628574..187628585, +
1.55e-98FFCP PHASE1:Hg19::chr6:132937900..132937907,-#_c444c6931f327308e73295794586b2b1p@chr6:132937900..132937907, -
1.55e-98FFCP PHASE2:Hg19::chr6:132937900..132937907,-#_c444c6931f327308e73295794586b2b1p@chr6:132937900..132937907, -
1.55e-98FFCP PHASE2:Hg19::chrX:110464144..110464149,+#_c444c6931f327308e73295794586b2b1p@chrX:110464144..110464149, +
1.55e-98FFCP PHASE1:Hg19::chr2:187628574..187628585,+#_c444c6931f327308e73295794586b2b1p@chr2:187628574..187628585, +
1.55e-98FFCP PHASE1:Hg19::chrX:110464144..110464149,+#_c444c6931f327308e73295794586b2b1p@chrX:110464144..110464149, +
4.22e-98FFCP PHASE2:Hg19::chr11:79784329..79784335,-#_9d476cd6ca3c89fe6c6c82236290322ep@chr11:79784329..79784335, -
4.22e-98FFCP PHASE1:Hg19::chr5:119669127..119669137,-#_9d476cd6ca3c89fe6c6c82236290322ep4@ENST00000514240
4.22e-98FFCP PHASE2:Hg19::chr5:119669127..119669137,-#_9d476cd6ca3c89fe6c6c82236290322ep4@ENST00000514240
4.22e-98FFCP PHASE1:Hg19::chr3:172166557..172166598,+#_9d476cd6ca3c89fe6c6c82236290322ep@chr3:172166557..172166598, +
4.22e-98FFCP PHASE2:Hg19::chr3:172166557..172166598,+#_9d476cd6ca3c89fe6c6c82236290322ep@chr3:172166557..172166598, +
4.22e-98FFCP PHASE1:Hg19::chr3:71777824..71777833,-#_9d476cd6ca3c89fe6c6c82236290322ep28@EIF4E3
4.22e-98FFCP PHASE1:Hg19::chr11:79784329..79784335,-#_9d476cd6ca3c89fe6c6c82236290322ep@chr11:79784329..79784335, -
4.22e-98FFCP PHASE2:Hg19::chr3:71777824..71777833,-#_9d476cd6ca3c89fe6c6c82236290322ep28@EIF4E3
7.79e-79FFCP PHASE2:Hg19::chr18:24435190..24435201,-#_ba8ad55101e5d35f7f138ff5edd4f99ap@chr18:24435190..24435201, -
7.79e-79FFCP PHASE1:Hg19::chr18:24435190..24435201,-#_ba8ad55101e5d35f7f138ff5edd4f99ap@chr18:24435190..24435201, -
7.41e-67FFCP PHASE1:Hg19::chr10:125454018..125454027,+#_1172bad77084887014d11251f683d3d4p@chr10:125454018..125454027, +
7.41e-67FFCP PHASE2:Hg19::chr10:125454018..125454027,+#_1172bad77084887014d11251f683d3d4p@chr10:125454018..125454027, +
1.04e-66FFCP PHASE1:Hg19::chr3:12225071..12225084,+#_96090d3883ccdc54f3c9b6705ca688bap15@SYN2
1.04e-66FFCP PHASE2:Hg19::chr3:12225071..12225084,+#_96090d3883ccdc54f3c9b6705ca688bap15@SYN2
7.73e-66FFCP PHASE1:Hg19::chrX:72432586..72432597,-#_4145dce13f7b26b7016907d23c0d2b53p@chrX:72432586..72432597, -
7.73e-66FFCP PHASE2:Hg19::chrX:72432586..72432597,-#_4145dce13f7b26b7016907d23c0d2b53p@chrX:72432586..72432597, -
2.02e-57FFCP PHASE2:Hg19::chr7:130745294..130745303,-#_b1e4420becd8abda6abc2ea3f68db575p@chr7:130745294..130745303, -
2.02e-57FFCP PHASE2:Hg19::chrX:13789306..13789315,-#_b1e4420becd8abda6abc2ea3f68db575p@chrX:13789306..13789315, -
2.02e-57FFCP PHASE1:Hg19::chrX:13789306..13789315,-#_b1e4420becd8abda6abc2ea3f68db575p@chrX:13789306..13789315, -
2.02e-57FFCP PHASE1:Hg19::chr7:130745294..130745303,-#_b1e4420becd8abda6abc2ea3f68db575p@chr7:130745294..130745303, -
2.69e-57FFCP PHASE2:Hg19::chr19:49932793..49932820,-#_b42af886966ac7d9ded83da0859c0816p@chr19:49932793..49932820, -
2.69e-57FFCP PHASE1:Hg19::chr19:49932793..49932820,-#_b42af886966ac7d9ded83da0859c0816p@chr19:49932793..49932820, -
3.58e-57FFCP PHASE2:Hg19::chr2:79601075..79601083,+#_169f0642acb24ca5b30468ac96276c9dp@chr2:79601075..79601083, +
3.58e-57FFCP PHASE1:Hg19::chr5:111964224..111964247,+#_169f0642acb24ca5b30468ac96276c9dp1@ENST00000507565
3.58e-57FFCP PHASE2:Hg19::chr5:111964224..111964247,+#_169f0642acb24ca5b30468ac96276c9dp1@ENST00000507565
3.58e-57FFCP PHASE1:Hg19::chr2:79601075..79601083,+#_169f0642acb24ca5b30468ac96276c9dp@chr2:79601075..79601083, +
4.77e-57FFCP PHASE1:Hg19::chr7:22158177..22158186,-#_d39c3bcd52b651df85bfb1e96ddd5cc7p@chr7:22158177..22158186, -
4.77e-57FFCP PHASE2:Hg19::chr7:22158177..22158186,-#_d39c3bcd52b651df85bfb1e96ddd5cc7p@chr7:22158177..22158186, -
6.36e-57FFCP PHASE2:Hg19::chr8:42981738..42981749,+#_df799ee581faf5df90822cb1258454cfp4@AK056481
6.36e-57FFCP PHASE1:Hg19::chr8:42981738..42981749,+#_df799ee581faf5df90822cb1258454cfp4@AK056481
8.82e-51FFCP PHASE1:Hg19::chr5:82155710..82155724,-#_33eabcca4ab673392dfc56d851d822b0p@chr5:82155710..82155724, -
8.82e-51FFCP PHASE2:Hg19::chr5:82155710..82155724,-#_33eabcca4ab673392dfc56d851d822b0p@chr5:82155710..82155724, -
1.14e-50FFCP PHASE2:Hg19::chr17:27901500..27901511,-#_b3ce97e7d1e9b64d4b75b136cbcd5fb1p25@GIT1
1.14e-50FFCP PHASE1:Hg19::chr15:43814895..43814906,+#_b3ce97e7d1e9b64d4b75b136cbcd5fb1p35@MAP1A
1.14e-50FFCP PHASE2:Hg19::chr15:43814895..43814906,+#_b3ce97e7d1e9b64d4b75b136cbcd5fb1p35@MAP1A
1.14e-50FFCP PHASE1:Hg19::chr17:27901500..27901511,-#_b3ce97e7d1e9b64d4b75b136cbcd5fb1p25@GIT1
2.42e-50FFCP PHASE1:Hg19::chr13:101712292..101712306,-#_55b63e9e2f7ce195dcbd37d70a88dab4p@chr13:101712292..101712306, -
2.42e-50FFCP PHASE2:Hg19::chr13:101712292..101712306,-#_55b63e9e2f7ce195dcbd37d70a88dab4p@chr13:101712292..101712306, -
2.74e-50FFCP PHASE2:Hg19::chr16:7240507..7240509,+#_5cba416437d4e732f54bae0bf6483f3bp@chr16:7240507..7240509, +
2.74e-50FFCP PHASE1:Hg19::chr19:49932741..49932746,-#_5cba416437d4e732f54bae0bf6483f3bp@chr19:49932741..49932746, -
2.74e-50FFCP PHASE1:Hg19::chr3:131756632..131756637,-#_5cba416437d4e732f54bae0bf6483f3bp11@CPNE4
2.74e-50FFCP PHASE2:Hg19::chr3:131756632..131756637,-#_5cba416437d4e732f54bae0bf6483f3bp11@CPNE4
2.74e-50FFCP PHASE1:Hg19::chr3:131756644..131756651,-#_5cba416437d4e732f54bae0bf6483f3bp13@CPNE4
2.74e-50FFCP PHASE2:Hg19::chr3:131756644..131756651,-#_5cba416437d4e732f54bae0bf6483f3bp13@CPNE4
2.74e-50FFCP PHASE1:Hg19::chr16:7240507..7240509,+#_5cba416437d4e732f54bae0bf6483f3bp@chr16:7240507..7240509, +
2.74e-50FFCP PHASE2:Hg19::chr19:49932741..49932746,-#_5cba416437d4e732f54bae0bf6483f3bp@chr19:49932741..49932746, -
3.11e-50FFCP PHASE2:Hg19::chr11:123502588..123502633,-#_99adba46d89ff3059de7a11a078290b3p16@SCN3B
3.11e-50FFCP PHASE1:Hg19::chr11:123502588..123502633,-#_99adba46d89ff3059de7a11a078290b3p16@SCN3B
4.0e-50FFCP PHASE2:Hg19::chr3:58552313..58552322,-#_2a4fbe385ba29a251193c0a231af2638p@chr3:58552313..58552322, -
4.0e-50FFCP PHASE1:Hg19::chr3:58552313..58552322,-#_2a4fbe385ba29a251193c0a231af2638p@chr3:58552313..58552322, -
4.52e-50FFCP PHASE1:Hg19::chr19:4772190..4772197,+#_09bdc6642d6e673f2e1850d469efd77cp@chr19:4772190..4772197, +
4.52e-50FFCP PHASE2:Hg19::chr21:27651095..27651104,+#_09bdc6642d6e673f2e1850d469efd77cp@chr21:27651095..27651104, +
4.52e-50FFCP PHASE1:Hg19::chr21:27650939..27650945,-#_09bdc6642d6e673f2e1850d469efd77cp@chr21:27650939..27650945, -
4.52e-50FFCP PHASE1:Hg19::chr18:24433388..24433397,-#_09bdc6642d6e673f2e1850d469efd77cp20@AQP4
4.52e-50FFCP PHASE2:Hg19::chr8:81570615..81570619,-#_09bdc6642d6e673f2e1850d469efd77cp@chr8:81570615..81570619, -
4.52e-50FFCP PHASE1:Hg19::chr1:99772065..99772074,+#_09bdc6642d6e673f2e1850d469efd77cp13@LPPR4
4.52e-50FFCP PHASE2:Hg19::chrX:152095682..152095708,-#_09bdc6642d6e673f2e1850d469efd77cp@chrX:152095682..152095708, -
4.52e-50FFCP PHASE1:Hg19::chr7:98460933..98460941,-#_09bdc6642d6e673f2e1850d469efd77cp19@TMEM130
4.52e-50FFCP PHASE1:Hg19::chrX:152095682..152095708,-#_09bdc6642d6e673f2e1850d469efd77cp@chrX:152095682..152095708, -
4.52e-50FFCP PHASE2:Hg19::chr7:98460933..98460941,-#_09bdc6642d6e673f2e1850d469efd77cp19@TMEM130
4.52e-50FFCP PHASE1:Hg19::chr8:81570615..81570619,-#_09bdc6642d6e673f2e1850d469efd77cp@chr8:81570615..81570619, -
4.52e-50FFCP PHASE1:Hg19::chr21:27651095..27651104,+#_09bdc6642d6e673f2e1850d469efd77cp@chr21:27651095..27651104, +
4.52e-50FFCP PHASE2:Hg19::chr20:44330800..44330802,-#_09bdc6642d6e673f2e1850d469efd77cp@chr20:44330800..44330802, -
4.52e-50FFCP PHASE2:Hg19::chr21:27650939..27650945,-#_09bdc6642d6e673f2e1850d469efd77cp@chr21:27650939..27650945, -
4.52e-50FFCP PHASE2:Hg19::chr8:26365361..26365372,-#_09bdc6642d6e673f2e1850d469efd77cp5@PNMA2
4.52e-50FFCP PHASE2:Hg19::chr19:4772190..4772197,+#_09bdc6642d6e673f2e1850d469efd77cp@chr19:4772190..4772197, +
4.52e-50FFCP PHASE2:Hg19::chr1:99772065..99772074,+#_09bdc6642d6e673f2e1850d469efd77cp13@LPPR4
4.52e-50FFCP PHASE1:Hg19::chr8:26365361..26365372,-#_09bdc6642d6e673f2e1850d469efd77cp5@PNMA2
4.52e-50FFCP PHASE2:Hg19::chr18:24433388..24433397,-#_09bdc6642d6e673f2e1850d469efd77cp20@AQP4
4.52e-50FFCP PHASE1:Hg19::chr20:44330800..44330802,-#_09bdc6642d6e673f2e1850d469efd77cp@chr20:44330800..44330802, -
5.15e-50FFCP PHASE1:Hg19::chr14:24037817..24037858,-#_dff6686a1c3c588c9a599bf78025d876p@chr14:24037817..24037858, -
5.15e-50FFCP PHASE2:Hg19::chr14:24037817..24037858,-#_dff6686a1c3c588c9a599bf78025d876p@chr14:24037817..24037858, -
6.61e-50FFCP PHASE1:Hg19::chr12:41234328..41234338,+#_5ba14aea95c9807c4415e5d63fc785bbp@chr12:41234328..41234338, +
6.61e-50FFCP PHASE2:Hg19::chr12:41234328..41234338,+#_5ba14aea95c9807c4415e5d63fc785bbp@chr12:41234328..41234338, +
3.19e-45FFCP PHASE1:Hg19::chr19:3294647..3294651,+#_473f6c8afbbd66640ad08416459817dfp@chr19:3294647..3294651, +
3.19e-45FFCP PHASE1:Hg19::chr12:79843202..79843213,+#_473f6c8afbbd66640ad08416459817dfp@chr12:79843202..79843213, +
3.19e-45FFCP PHASE2:Hg19::chr12:79843202..79843213,+#_473f6c8afbbd66640ad08416459817dfp@chr12:79843202..79843213, +
3.19e-45FFCP PHASE2:Hg19::chr19:3294647..3294651,+#_473f6c8afbbd66640ad08416459817dfp@chr19:3294647..3294651, +
6.26e-45FFCP PHASE1:Hg19::chr5:63258078..63258088,-#_47025a3c549e81b8cfdf8f064ac8725fp6@HTR1A
6.26e-45FFCP PHASE2:Hg19::chr8:27316567..27316576,+#_47025a3c549e81b8cfdf8f064ac8725fp@chr8:27316567..27316576, +
6.26e-45FFCP PHASE2:Hg19::chr5:63258078..63258088,-#_47025a3c549e81b8cfdf8f064ac8725fp6@HTR1A
6.26e-45FFCP PHASE1:Hg19::chr8:27316567..27316576,+#_47025a3c549e81b8cfdf8f064ac8725fp@chr8:27316567..27316576, +
6.26e-45FFCP PHASE2:Hg19::chr9:87426979..87426990,+#_47025a3c549e81b8cfdf8f064ac8725fp54@NTRK2
6.26e-45FFCP PHASE1:Hg19::chr9:87426979..87426990,+#_47025a3c549e81b8cfdf8f064ac8725fp54@NTRK2
7.83e-45FFCP PHASE1:Hg19::chr1:160112787..160112798,+#_d216e154295d162d125fd83ba361c149p12@ATP1A2
7.83e-45FFCP PHASE2:Hg19::chr2:101965038..101965076,-#_d216e154295d162d125fd83ba361c149p@chr2:101965038..101965076, -
7.83e-45FFCP PHASE1:Hg19::chr5:63258105..63258124,-#_d216e154295d162d125fd83ba361c149p2@HTR1A
7.83e-45FFCP PHASE2:Hg19::chr1:160112787..160112798,+#_d216e154295d162d125fd83ba361c149p12@ATP1A2
7.83e-45FFCP PHASE2:Hg19::chr5:63258105..63258124,-#_d216e154295d162d125fd83ba361c149p2@HTR1A
7.83e-45FFCP PHASE1:Hg19::chr2:101965038..101965076,-#_d216e154295d162d125fd83ba361c149p@chr2:101965038..101965076, -

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