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{{UBERON
{{UBERON
|id=UBERON:0005562
|alt_id=
|name=thymus primordium
|namespace=
|def="A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]." [ZFA:0001077]
|xref=EFO:0003622;;EHDAA2:0002023;;EHDAA:2969;;EMAPA:17523;;EMAPA:18536;;TAO:0001077;;ZFA:0001077
|is_a=UBERON:0001048;;UBERON:0003351
|synonym="thymic primordium" EXACT [Obol:automatic];;"thymic rudiment" EXACT [ZFA:0001077]
|comment=Editor notes: we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Development notes: Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. Taxon notes: variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals[ISBN-10:0781714125]
|comment=Editor notes: we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Development notes: Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. Taxon notes: variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals[ISBN-10:0781714125]
|alt_id=
|disjoint_from=
|union_of=
|created_by=
|created_by=
|obo_creation_date=
|def="A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]." [ZFA:0001077]
|subset=vertebrate_core
|derives_from=
|derives_from=
|develops_from=UBERON:0007690
|develops_from=UBERON:0007690
|disjoint_from=
|has_quality=
|has_quality=
|id=UBERON:0005562
|is_a=UBERON:0001048 ;;UBERON:0003351
|is_obsolete=
|located_in=
|located_in=
|name=thymus primordium
|namespace=FANTOM
|obo_creation_date=
|part_of=UBERON:0000974;;UBERON:0002405;;UBERON:0003295
|part_of=UBERON:0000974;;UBERON:0002405;;UBERON:0003295
|preceded_by=
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl;;UBPROP:0000001 "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]" xsd:string
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl;;UBPROP:0000001 "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]" xsd:string
|is_obsolete=
|subset=vertebrate_core
|preceded_by=
|synonym="thymic primordium" EXACT [Obol:automatic];;"thymic rudiment" EXACT [ZFA:0001077]
|union_of=
|xref=EFO:0003622;;EHDAA2:0002023;;EHDAA:2969;;EMAPA:17523;;EMAPA:18536;;TAO:0001077;;ZFA:0001077
}}
}}

Latest revision as of 17:54, 12 September 2014

Name:thymus primordium
Namespace:FANTOM
Definition:"A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]." [ZFA:0001077]
Xrefs:
links:

EFO:0003622
EHDAA2:0002023
EHDAA:2969
EMAPA:17523
EMAPA:18536
TAO:0001077

ZFA:0001077
Synonyms: "thymic primordium" EXACT [Obol:automatic]
"thymic rudiment" EXACT [ZFA:0001077]
Comments:Editor notes: we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Development notes: Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. Taxon notes: variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals[ISBN-10:0781714125]
Subset: vertebrate_core

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:0001048(primordium),UBERON:0003351(pharyngeal epithelium)
develops_from:UBERON:0007690(early pharyngeal endoderm)
part_of:UBERON:0000974(neck),UBERON:0002405(immune system),UBERON:0003295(pharyngeal gland)



Children

develops from:UBERON:0002370 (thymus)

Ontology Tree: Loaded from BioPortal

Ontorolgy tree(Small window open)

FF samples<br>It includes FANTOM5 samples that overlay the Uberon ontology



Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with UBERON:0005562 (thymus primordium), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

P-valueFFCPShort description
6.94e-147FFCP PHASE2:Hg19::chr14:22928012..22928031,+#_0273faff036d23caa0d105641de9c797p3@uc001wea.3, p3@uc010ajt.2, p3@uc010aju.1
6.94e-147FFCP PHASE1:Hg19::chr14:22928012..22928031,+#_0273faff036d23caa0d105641de9c797p3@uc001wea.3, p3@uc010ajt.2, p3@uc010aju.1
8.91e-111FFCP PHASE1:Hg19::chr14:22927984..22927999,+#_f975cfd9f3472c82de4ae00d46b2b00ep4@uc001wea.3, p4@uc010ajt.2, p4@uc010aju.1
8.91e-111FFCP PHASE2:Hg19::chr14:22927984..22927999,+#_f975cfd9f3472c82de4ae00d46b2b00ep4@uc001wea.3, p4@uc010ajt.2, p4@uc010aju.1
1.55e-98FFCP PHASE1:Hg19::chr2:87018900..87018905,+#_7897f2c0d8afffba533695b9bee075bep@chr2:87018900..87018905, +
1.55e-98FFCP PHASE1:Hg19::chr15:58069758..58069762,+#_7897f2c0d8afffba533695b9bee075bep@chr15:58069758..58069762, +
1.55e-98FFCP PHASE1:Hg19::chr11:36622593..36622605,+#_7897f2c0d8afffba533695b9bee075bep@chr11:36622593..36622605, +
1.55e-98FFCP PHASE1:Hg19::chr12:123636839..123636885,-#_7897f2c0d8afffba533695b9bee075bep@chr12:123636839..123636885, -
1.55e-98FFCP PHASE1:Hg19::chr1:158259849..158259854,+#_7897f2c0d8afffba533695b9bee075bep11@CD1C
1.55e-98FFCP PHASE1:Hg19::chr1:200500161..200500173,-#_7897f2c0d8afffba533695b9bee075bep@chr1:200500161..200500173, -
1.55e-98FFCP PHASE1:Hg19::chr1:204494413..204494420,+#_7897f2c0d8afffba533695b9bee075bep17@MDM4
1.55e-98FFCP PHASE1:Hg19::chr11:6953654..6953661,+#_7897f2c0d8afffba533695b9bee075bep5@ZNF215
1.55e-98FFCP PHASE1:Hg19::chr2:227771357..227771363,+#_7897f2c0d8afffba533695b9bee075bep10@RHBDD1
1.55e-98FFCP PHASE1:Hg19::chr10:11486829..11486836,+#_7897f2c0d8afffba533695b9bee075bep@chr10:11486829..11486836, +
1.55e-98FFCP PHASE1:Hg19::chr2:233184654..233184661,-#_7897f2c0d8afffba533695b9bee075bep@chr2:233184654..233184661, -
1.55e-98FFCP PHASE1:Hg19::chr10:11486877..11486886,+#_7897f2c0d8afffba533695b9bee075bep@chr10:11486877..11486886, +
1.55e-98FFCP PHASE1:Hg19::chr10:115022988..115023001,+#_7897f2c0d8afffba533695b9bee075bep@chr10:115022988..115023001, +
1.55e-98FFCP PHASE1:Hg19::chr10:115023005..115023015,+#_7897f2c0d8afffba533695b9bee075bep@chr10:115023005..115023015, +
1.55e-98FFCP PHASE1:Hg19::chr15:60131355..60131365,-#_7897f2c0d8afffba533695b9bee075bep@chr15:60131355..60131365, -
1.55e-98FFCP PHASE1:Hg19::chr16:74359040..74359071,+#_7897f2c0d8afffba533695b9bee075bep@chr16:74359040..74359071, +
1.55e-98FFCP PHASE1:Hg19::chr10:115023055..115023072,+#_7897f2c0d8afffba533695b9bee075bep@chr10:115023055..115023072, +
1.55e-98FFCP PHASE1:Hg19::chr10:115023094..115023106,+#_7897f2c0d8afffba533695b9bee075bep@chr10:115023094..115023106, +
1.55e-98FFCP PHASE1:Hg19::chr17:76274572..76274581,-#_7897f2c0d8afffba533695b9bee075bep4@ENST00000374945
1.55e-98FFCP PHASE1:Hg19::chr12:48227243..48227269,+#_7897f2c0d8afffba533695b9bee075bep@chr12:48227243..48227269, +
1.55e-98FFCP PHASE1:Hg19::chr3:155273127..155273136,-#_7897f2c0d8afffba533695b9bee075bep4@AK093601
1.55e-98FFCP PHASE1:Hg19::chr12:123634449..123634460,-#_7897f2c0d8afffba533695b9bee075bep25@PITPNM2
1.55e-98FFCP PHASE1:Hg19::chr2:87018380..87018390,-#_7897f2c0d8afffba533695b9bee075bep6@CD8A
1.55e-98FFCP PHASE1:Hg19::chr3:34517538..34517551,+#_7897f2c0d8afffba533695b9bee075bep@chr3:34517538..34517551, +
1.55e-98FFCP PHASE1:Hg19::chr11:36589389..36589398,-#_7897f2c0d8afffba533695b9bee075bep@chr11:36589389..36589398, -
1.55e-98FFCP PHASE1:Hg19::chr17:80866179..80866188,+#_7897f2c0d8afffba533695b9bee075bep@chr17:80866179..80866188, +
1.55e-98FFCP PHASE1:Hg19::chr1:204507243..204507252,+#_7897f2c0d8afffba533695b9bee075bep19@MDM4
1.55e-98FFCP PHASE1:Hg19::chr15:56940722..56940731,+#_7897f2c0d8afffba533695b9bee075bep@chr15:56940722..56940731, +
1.55e-98FFCP PHASE1:Hg19::chr15:58069384..58069408,+#_7897f2c0d8afffba533695b9bee075bep@chr15:58069384..58069408, +
1.55e-98FFCP PHASE1:Hg19::chr1:158226030..158226041,+#_7897f2c0d8afffba533695b9bee075bep@chr1:158226030..158226041, +
1.55e-98FFCP PHASE1:Hg19::chr3:35683004..35683015,+#_7897f2c0d8afffba533695b9bee075bep42@ARPP21
1.55e-98FFCP PHASE1:Hg19::chr1:204494427..204494436,+#_7897f2c0d8afffba533695b9bee075bep15@MDM4
1.55e-98FFCP PHASE1:Hg19::chr1:2084380..2084413,-#_7897f2c0d8afffba533695b9bee075bep@chr1:2084380..2084413, -
1.55e-98FFCP PHASE1:Hg19::chr1:158170478..158170491,-#_7897f2c0d8afffba533695b9bee075bep@chr1:158170478..158170491, -
1.55e-98FFCP PHASE1:Hg19::chr12:133414662..133414671,-#_7897f2c0d8afffba533695b9bee075bep@chr12:133414662..133414671, -
1.55e-98FFCP PHASE1:Hg19::chr20:58830826..58830835,+#_7897f2c0d8afffba533695b9bee075bep@chr20:58830826..58830835, +
1.55e-98FFCP PHASE1:Hg19::chr2:233102726..233102734,+#_7897f2c0d8afffba533695b9bee075bep@chr2:233102726..233102734, +
1.55e-98FFCP PHASE1:Hg19::chr15:57017749..57017755,-#_7897f2c0d8afffba533695b9bee075bep@chr15:57017749..57017755, -
1.55e-98FFCP PHASE1:Hg19::chr1:44035233..44035242,+#_7897f2c0d8afffba533695b9bee075bep@chr1:44035233..44035242, +
1.55e-98FFCP PHASE1:Hg19::chr10:26726728..26726731,+#_7897f2c0d8afffba533695b9bee075bep17@APBB1IP
1.55e-98FFCP PHASE1:Hg19::chr20:30272266..30272271,-#_7897f2c0d8afffba533695b9bee075bep@chr20:30272266..30272271, -
1.55e-98FFCP PHASE1:Hg19::chr20:58830799..58830808,+#_7897f2c0d8afffba533695b9bee075bep@chr20:58830799..58830808, +
1.55e-98FFCP PHASE1:Hg19::chr18:13437980..13437986,+#_7897f2c0d8afffba533695b9bee075bep@chr18:13437980..13437986, +
1.55e-98FFCP PHASE1:Hg19::chr12:47205180..47205187,+#_7897f2c0d8afffba533695b9bee075bep@chr12:47205180..47205187, +
1.55e-98FFCP PHASE1:Hg19::chr2:87017428..87017437,+#_7897f2c0d8afffba533695b9bee075bep@chr2:87017428..87017437, +
1.55e-98FFCP PHASE1:Hg19::chr2:57846504..57846542,+#_7897f2c0d8afffba533695b9bee075bep@chr2:57846504..57846542, +
1.55e-98FFCP PHASE1:Hg19::chr12:123607146..123607168,-#_7897f2c0d8afffba533695b9bee075bep@chr12:123607146..123607168, -
1.55e-98FFCP PHASE1:Hg19::chr1:199026759..199026762,+#_7897f2c0d8afffba533695b9bee075bep@chr1:199026759..199026762, +
1.55e-98FFCP PHASE1:Hg19::chr1:158332631..158332640,+#_7897f2c0d8afffba533695b9bee075bep@chr1:158332631..158332640, +
1.55e-98FFCP PHASE1:Hg19::chr13:99628369..99628374,-#_7897f2c0d8afffba533695b9bee075bep@chr13:99628369..99628374, -
1.55e-98FFCP PHASE1:Hg19::chr3:34517741..34517784,+#_7897f2c0d8afffba533695b9bee075bep@chr3:34517741..34517784, +
1.55e-98FFCP PHASE1:Hg19::chr12:123559773..123559784,-#_7897f2c0d8afffba533695b9bee075bep@chr12:123559773..123559784, -
1.55e-98FFCP PHASE1:Hg19::chr1:158260453..158260459,-#_7897f2c0d8afffba533695b9bee075bep@chr1:158260453..158260459, -
1.55e-98FFCP PHASE1:Hg19::chr15:60131313..60131324,-#_7897f2c0d8afffba533695b9bee075bep@chr15:60131313..60131324, -
1.55e-98FFCP PHASE1:Hg19::chr12:123559708..123559720,-#_7897f2c0d8afffba533695b9bee075bep@chr12:123559708..123559720, -
1.55e-98FFCP PHASE1:Hg19::chr15:99071828..99071840,+#_7897f2c0d8afffba533695b9bee075bep@chr15:99071828..99071840, +
1.55e-98FFCP PHASE1:Hg19::chr1:160643269..160643276,+#_7897f2c0d8afffba533695b9bee075bep5@ENST00000443928
1.55e-98FFCP PHASE1:Hg19::chr12:59432175..59432191,+#_7897f2c0d8afffba533695b9bee075bep@chr12:59432175..59432191, +
1.55e-98FFCP PHASE1:Hg19::chr1:158260649..158260652,+#_7897f2c0d8afffba533695b9bee075bep13@CD1C
1.55e-98FFCP PHASE1:Hg19::chr15:60131337..60131352,-#_7897f2c0d8afffba533695b9bee075bep@chr15:60131337..60131352, -
1.55e-98FFCP PHASE1:Hg19::chr14:98229095..98229108,-#_7897f2c0d8afffba533695b9bee075bep1@ENST00000555187
1.55e-98FFCP PHASE1:Hg19::chr15:56940732..56940741,+#_7897f2c0d8afffba533695b9bee075bep@chr15:56940732..56940741, +
1.55e-98FFCP PHASE1:Hg19::chr14:22942319..22942322,+#_7897f2c0d8afffba533695b9bee075bep4@uc001wec.2
1.55e-98FFCP PHASE1:Hg19::chr3:19007717..19007728,+#_7897f2c0d8afffba533695b9bee075bep@chr3:19007717..19007728, +
1.55e-98FFCP PHASE1:Hg19::chr13:99628347..99628352,-#_7897f2c0d8afffba533695b9bee075bep@chr13:99628347..99628352, -
1.55e-98FFCP PHASE1:Hg19::chr2:57926329..57926337,-#_7897f2c0d8afffba533695b9bee075bep@chr2:57926329..57926337, -
1.55e-98FFCP PHASE1:Hg19::chr3:35682974..35682982,+#_7897f2c0d8afffba533695b9bee075bep45@ARPP21
1.55e-98FFCP PHASE1:Hg19::chr1:44035057..44035068,+#_7897f2c0d8afffba533695b9bee075bep@chr1:44035057..44035068, +
1.55e-98FFCP PHASE1:Hg19::chr2:242080265..242080277,-#_7897f2c0d8afffba533695b9bee075bep20@PASK
1.55e-98FFCP PHASE1:Hg19::chr17:4090402..4090406,-#_7897f2c0d8afffba533695b9bee075bep@chr17:4090402..4090406, -
1.55e-98FFCP PHASE1:Hg19::chr15:58920068..58920073,-#_7897f2c0d8afffba533695b9bee075bep@chr15:58920068..58920073, -
1.55e-98FFCP PHASE1:Hg19::chr2:227771044..227771054,+#_7897f2c0d8afffba533695b9bee075bep9@RHBDD1
1.55e-98FFCP PHASE1:Hg19::chr12:123560793..123560802,+#_7897f2c0d8afffba533695b9bee075bep@chr12:123560793..123560802, +
1.55e-98FFCP PHASE1:Hg19::chr13:99628323..99628332,-#_7897f2c0d8afffba533695b9bee075bep@chr13:99628323..99628332, -
1.55e-98FFCP PHASE1:Hg19::chr12:123560608..123560615,-#_7897f2c0d8afffba533695b9bee075bep24@PITPNM2
1.55e-98FFCP PHASE1:Hg19::chr12:133413547..133413557,-#_7897f2c0d8afffba533695b9bee075bep13@POLE
1.55e-98FFCP PHASE1:Hg19::chr1:55776022..55776029,-#_7897f2c0d8afffba533695b9bee075bep@chr1:55776022..55776029, -
1.55e-98FFCP PHASE1:Hg19::chr12:123627753..123627760,+#_7897f2c0d8afffba533695b9bee075bep@chr12:123627753..123627760, +
1.55e-98FFCP PHASE1:Hg19::chr17:76274646..76274658,-#_7897f2c0d8afffba533695b9bee075bep2@ENST00000374945
1.55e-98FFCP PHASE1:Hg19::chr2:162762361..162762364,+#_7897f2c0d8afffba533695b9bee075bep@chr2:162762361..162762364, +
1.55e-98FFCP PHASE1:Hg19::chr20:58830811..58830825,+#_7897f2c0d8afffba533695b9bee075bep@chr20:58830811..58830825, +
1.55e-98FFCP PHASE1:Hg19::chr15:58069582..58069594,+#_7897f2c0d8afffba533695b9bee075bep@chr15:58069582..58069594, +
1.55e-98FFCP PHASE1:Hg19::chr10:72542272..72542281,-#_7897f2c0d8afffba533695b9bee075bep6@C10orf27
1.55e-98FFCP PHASE1:Hg19::chr1:158301280..158301298,+#_7897f2c0d8afffba533695b9bee075bep@chr1:158301280..158301298, +
1.55e-98FFCP PHASE1:Hg19::chr20:58833004..58833011,+#_7897f2c0d8afffba533695b9bee075bep@chr20:58833004..58833011, +
1.55e-98FFCP PHASE1:Hg19::chr13:99628388..99628399,-#_7897f2c0d8afffba533695b9bee075bep@chr13:99628388..99628399, -
1.55e-98FFCP PHASE1:Hg19::chr16:49633750..49633778,-#_7897f2c0d8afffba533695b9bee075bep@chr16:49633750..49633778, -
1.55e-98FFCP PHASE1:Hg19::chr12:48225126..48225164,+#_7897f2c0d8afffba533695b9bee075bep1@ENST00000548564, p1@ENST00000550720, p1@ENST00000550909
1.55e-98FFCP PHASE1:Hg19::chr1:194245598..194245600,-#_7897f2c0d8afffba533695b9bee075bep@chr1:194245598..194245600, -
1.55e-98FFCP PHASE1:Hg19::chr1:160643289..160643296,+#_7897f2c0d8afffba533695b9bee075bep4@ENST00000443928
1.55e-98FFCP PHASE1:Hg19::chr15:58069597..58069604,+#_7897f2c0d8afffba533695b9bee075bep@chr15:58069597..58069604, +
1.55e-98FFCP PHASE1:Hg19::chr1:158303678..158303720,-#_7897f2c0d8afffba533695b9bee075bep@chr1:158303678..158303720, -
1.55e-98FFCP PHASE1:Hg19::chr1:55776031..55776038,-#_7897f2c0d8afffba533695b9bee075bep@chr1:55776031..55776038, -
1.55e-98FFCP PHASE1:Hg19::chr19:28877072..28877084,-#_7897f2c0d8afffba533695b9bee075bep@chr19:28877072..28877084, -
1.55e-98FFCP PHASE1:Hg19::chr1:32314477..32314482,+#_7897f2c0d8afffba533695b9bee075bep@chr1:32314477..32314482, +
1.55e-98FFCP PHASE1:Hg19::chr11:8954087..8954092,-#_7897f2c0d8afffba533695b9bee075bep1@AB527792










Property "Property value" (as page type) with input value "UBPROP:0000001 "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]" xsd:string" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.

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