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UBERON:0003104

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Name:mesenchyme
Namespace:FANTOM
Definition:"Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]." [BTO:0001393, Wikipedia:Mesenchyme, ZFIN:curator]
Xrefs:
links:

AAO:0010427
AEO:0000145
BTO:0001393
EHDAA2:0003145
EV:0100007
[1]
[2]
ncithesaurus:Mesenchyme
TAO:0000393
VHOG:0000170
XAO:0003046

ZFA:0000393
Synonyms: "mesenchyma" RELATED LATIN [Wikipedia:Mesenchyme]
"mesenchymal tissue" EXACT []
"mesenchyme tissue" EXACT []
"portion of mesenchymal tissue" EXACT []
"portion of mesenchyme tissue" EXACT []
Comments:Editors notes: the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
Alt_id: UBERON:XAO_0003046-ZFA_0000393
Subset: uberon_slim
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:0000479(tissue)
part_of:UBERON:0009142(entire embryonic mesenchyme)



Children

is a:UBERON:0003422 (mesenchyme of umbilical cord),UBERON:0003918 (kidney mesenchyme),UBERON:0004161 (septum transversum),UBERON:0004208 (nephrogenic mesenchyme),UBERON:0005253 (head mesenchyme),UBERON:0005256 (trunk mesenchyme),UBERON:0006258 (lateral plate mesenchyme),UBERON:0006293 (spleen primordium),UBERON:0007524 (dense mesenchyme tissue),UBERON:0007530 (migrating mesenchyme population),UBERON:0009526 (maxillary process mesenchyme),UBERON:0009749 (limb mesenchyme),UBERON:0009751 (cardiac mesenchyme),UBERON:0009891 (facial mesenchyme),UBERON:0010083 (future dermis),UBERON:0014387 (mesenchyme derived from neural crest)
develops from:UBERON:0001046 (hindgut),UBERON:0002514 (intramembranous bone)

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)

  • 10813-111B3 (normal embryonic palatal mesenchymal cell line:HEPM)
  • 11214-116A8 (Mesenchymal stem cells - umbilical, donor0)
  • 11539-120A9 (Mesenchymal Stem Cells - umbilical, donor1)
  • 11548-120B9 (Mesenchymal Stem Cells - Wharton's Jelly, donor1)
  • 11549-120C1 (Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor1)
  • 11619-122A8 (Mesenchymal Stem Cells - umbilical, donor2)
  • 11628-122B8
  • 11629-122B9 (Multipotent Cord Blood Unrestricted Somatic Stem Cells, donor2)
  • 11700-123A8 (Mesenchymal Stem Cells - umbilical, donor3)


Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with UBERON:0003104 (mesenchyme), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data


P-valueFFCPShort description
6.46e-31FFCP PHASE1:Mm9::chr4:95246108..95246119,+#_0d1bb52f9e519e04e8d6fbf0402aa449p4@Fggy
6.46e-31FFCP PHASE2:Mm9::chr4:95246108..95246119,+#_0d1bb52f9e519e04e8d6fbf0402aa449p4@Fggy
1.91e-30FFCP PHASE2:Hg19::chr8:30242040..30242045,+#_6ca15889149aa8712435b6b0d96b8530p2@RBPMS
1.91e-30FFCP PHASE1:Hg19::chr8:30242040..30242045,+#_6ca15889149aa8712435b6b0d96b8530p2@RBPMS
2.99e-28FFCP PHASE1:Hg19::chr8:30242048..30242064,+#_8f05d5693ec71cdc44b81f1165c554bcp1@RBPMS
2.99e-28FFCP PHASE2:Hg19::chr8:30242048..30242064,+#_8f05d5693ec71cdc44b81f1165c554bcp1@RBPMS
5.64e-28FFCP PHASE2:Hg19::chr8:30241934..30241945,+#_4bbcc577702ee1b5f3e91f7444c57472p3@RBPMS
5.64e-28FFCP PHASE1:Hg19::chr8:30241934..30241945,+#_4bbcc577702ee1b5f3e91f7444c57472p3@RBPMS
6.23e-28FFCP PHASE1:Mm9::chr6:34129226..34129246,+#_42c98e2c8e8ce253758cd386bbf5cba4p2@ENSMUST00000145644
6.23e-28FFCP PHASE2:Mm9::chr6:34129226..34129246,+#_42c98e2c8e8ce253758cd386bbf5cba4p2@ENSMUST00000145644
6.8e-28FFCP PHASE1:Mm9::chr8:73247943..73247958,+#_323160c25c633476891171e1a8dd3559p3@Pde4c
6.8e-28FFCP PHASE2:Mm9::chr8:73247943..73247958,+#_323160c25c633476891171e1a8dd3559p3@Pde4c
2.88e-27FFCP PHASE1:Hg19::chr11:114167164..114167190,+#_8e1c43b848111e2eefb76f23353895e7p2@NNMT
2.88e-27FFCP PHASE2:Hg19::chr11:114167164..114167190,+#_8e1c43b848111e2eefb76f23353895e7p2@NNMT
3.05e-27FFCP PHASE1:Mm9::chr9:44611035..44611044,-#_ac1cde4d303f967c913a226cca562afbp4@Ttc36
3.05e-27FFCP PHASE2:Mm9::chr9:44611035..44611044,-#_ac1cde4d303f967c913a226cca562afbp4@Ttc36
5.08e-27FFCP PHASE2:Hg19::chr19:48894762..48894830,-#_a00594996c7d7eeb847c486a7553c907p1@KDELR1
5.08e-27FFCP PHASE1:Hg19::chr19:48894762..48894830,-#_a00594996c7d7eeb847c486a7553c907p1@KDELR1
1.09e-26FFCP PHASE2:Mm9::chr11:60622345..60622377,-#_efe0067227b485d98c069a964c81886ap@chr11:60622345..60622377, -
1.09e-26FFCP PHASE1:Mm9::chr11:60622345..60622377,-#_efe0067227b485d98c069a964c81886ap@chr11:60622345..60622377, -
1.25e-26FFCP PHASE1:Mm9::chr10:88996274..88996286,-#_d626bf6db69982a846847032924f7a7bp4@Nr1h4
1.25e-26FFCP PHASE2:Mm9::chr10:88996274..88996286,-#_d626bf6db69982a846847032924f7a7bp4@Nr1h4
1.81e-26FFCP PHASE1:Mm9::chr11:7097807..7097814,+#_c5f3382358460f0b3f93f8f97a71c5cfp2@Igfbp1
1.81e-26FFCP PHASE2:Mm9::chr11:7097807..7097814,+#_c5f3382358460f0b3f93f8f97a71c5cfp2@Igfbp1
2.8e-26FFCP PHASE1:Mm9::chr19:12707997..12708015,+#_55b8bcff8242360f3dec1649c419ed3fp1@Glyat
2.8e-26FFCP PHASE2:Mm9::chr19:12707997..12708015,+#_55b8bcff8242360f3dec1649c419ed3fp1@Glyat
3.19e-26FFCP PHASE2:Mm9::chr13:23931270..23931311,+#_ea04df79573d5bd6753a0164d9906a95p2@Slc17a3
3.19e-26FFCP PHASE1:Mm9::chr13:23931270..23931311,+#_ea04df79573d5bd6753a0164d9906a95p2@Slc17a3
3.4e-26FFCP PHASE1:Mm9::chr16:37621995..37622022,-#_c50f994e9b930db751a30e2a608e8cd4p@chr16:37621995..37622022, -
3.4e-26FFCP PHASE2:Mm9::chr16:37621995..37622022,-#_c50f994e9b930db751a30e2a608e8cd4p@chr16:37621995..37622022, -
4.15e-26FFCP PHASE2:Hg19::chr11:114167202..114167221,+#_7ee61ef3bc6592109c1dd41f68327426p3@NNMT
4.15e-26FFCP PHASE1:Hg19::chr11:114167202..114167221,+#_7ee61ef3bc6592109c1dd41f68327426p3@NNMT
6.21e-26FFCP PHASE2:Mm9::chr13:23931467..23931489,+#_1f969e856e94e4d435f617252d0f448ep3@Slc17a3
6.21e-26FFCP PHASE1:Mm9::chr13:23931467..23931489,+#_1f969e856e94e4d435f617252d0f448ep3@Slc17a3
7.91e-26FFCP PHASE2:Mm9::chr4:96330769..96330789,-#_c630ab23f37af7e383a05d2311ada4f8p2@Cyp2j5
7.91e-26FFCP PHASE1:Mm9::chr4:96330769..96330789,-#_c630ab23f37af7e383a05d2311ada4f8p2@Cyp2j5
1.05e-25FFCP PHASE2:Mm9::chr1:142079981..142079992,-#_6d2b88f0f6a3814ea50e0fbddd3acc3dp3@Cfh
1.05e-25FFCP PHASE1:Mm9::chr1:142079981..142079992,-#_6d2b88f0f6a3814ea50e0fbddd3acc3dp3@Cfh
1.26e-25FFCP PHASE1:Hg19::chr7:6523755..6523829,-#_8c134748f779a14638ec91b30b1c4e53p1@DAGLB, p1@KDELR2
1.26e-25FFCP PHASE2:Hg19::chr7:6523755..6523829,-#_8c134748f779a14638ec91b30b1c4e53p1@DAGLB, p1@KDELR2
1.32e-25FFCP PHASE2:Mm9::chr16:37580223..37580237,+#_f2b2fc848a8e355e4e2650aae02f918bp4@Hgd
1.32e-25FFCP PHASE1:Mm9::chr16:37580223..37580237,+#_f2b2fc848a8e355e4e2650aae02f918bp4@Hgd
1.63e-25FFCP PHASE1:Mm9::chr1:141398256..141398267,+#_100ca00f6b2e29d68a87cf33e86b2fadp3@F13b
1.63e-25FFCP PHASE2:Mm9::chr1:141398256..141398267,+#_100ca00f6b2e29d68a87cf33e86b2fadp3@F13b
1.79e-25FFCP PHASE2:Mm9::chr4:95246137..95246153,+#_b135e1781ceca25c8cbabe8d0e26b5cfp3@Fggy
1.79e-25FFCP PHASE1:Mm9::chr4:95246137..95246153,+#_b135e1781ceca25c8cbabe8d0e26b5cfp3@Fggy
2.13e-25FFCP PHASE2:Mm9::chr15:82624876..82624892,-#_70b5be46c3f7ee470b6749ceca380ec0p5@Cyp2d26
2.13e-25FFCP PHASE1:Mm9::chr15:82624876..82624892,-#_70b5be46c3f7ee470b6749ceca380ec0p5@Cyp2d26
2.19e-25FFCP PHASE2:Mm9::chr10:95305558..95305580,-#_434462b8d5a4d3644977484081e1025fp@chr10:95305558..95305580, -
2.19e-25FFCP PHASE1:Mm9::chr10:95305558..95305580,-#_434462b8d5a4d3644977484081e1025fp@chr10:95305558..95305580, -
2.31e-25FFCP PHASE1:Hg19::chr14:35183837..35183867,-#_933eeb3fb718ced420947367b4de589ap2@CFL2
2.31e-25FFCP PHASE2:Hg19::chr14:35183837..35183867,-#_933eeb3fb718ced420947367b4de589ap2@CFL2
2.74e-25FFCP PHASE1:Hg19::chr5:148521286..148521377,+#_b546599d4402a5a0496ff15857a92671p2@ABLIM3
2.74e-25FFCP PHASE2:Hg19::chr5:148521286..148521377,+#_b546599d4402a5a0496ff15857a92671p2@ABLIM3
2.77e-25FFCP PHASE2:Mm9::chr9:44609886..44609901,-#_7e01e16957a28223677915ebd471be08p@chr9:44609886..44609901, -
2.77e-25FFCP PHASE1:Mm9::chr9:44609886..44609901,-#_7e01e16957a28223677915ebd471be08p@chr9:44609886..44609901, -
4.16e-25FFCP PHASE1:Mm9::chr4:150283537..150283568,-#_af0ff882a507956c3703aa0aec62644ap5@Park7
4.16e-25FFCP PHASE2:Mm9::chr4:150283537..150283568,-#_af0ff882a507956c3703aa0aec62644ap5@Park7
4.54e-25FFCP PHASE2:Mm9::chr12:58298278..58298292,-#_493f1ab84007bcc2b4709f34451bf9ebp4@Slc25a21
4.54e-25FFCP PHASE1:Mm9::chr12:58298278..58298292,-#_493f1ab84007bcc2b4709f34451bf9ebp4@Slc25a21
4.55e-25FFCP PHASE1:Mm9::chr9:44609861..44609874,-#_bc7b26e2dd4d22d2d6b732033d2fd8a7p@chr9:44609861..44609874, -
4.55e-25FFCP PHASE2:Mm9::chr9:44609861..44609874,-#_bc7b26e2dd4d22d2d6b732033d2fd8a7p@chr9:44609861..44609874, -
4.85e-25FFCP PHASE2:Mm9::chr4:140176541..140176565,-#_2e26eea4b9a2c3f444bc915c573202e5p@chr4:140176541..140176565, -
4.85e-25FFCP PHASE1:Mm9::chr4:140176541..140176565,-#_2e26eea4b9a2c3f444bc915c573202e5p@chr4:140176541..140176565, -
5.05e-25FFCP PHASE2:Hg19::chr2:27255806..27255879,+#_55bb8b55afabb431e1c1b39537a89459p1@TMEM214
5.05e-25FFCP PHASE1:Hg19::chr2:27255806..27255879,+#_55bb8b55afabb431e1c1b39537a89459p1@TMEM214
5.09e-25FFCP PHASE1:Mm9::chr15:99733367..99733388,+#_4679f11546fc00992f2359e54e12448fp@chr15:99733367..99733388, +
5.09e-25FFCP PHASE2:Mm9::chr15:99733367..99733388,+#_4679f11546fc00992f2359e54e12448fp@chr15:99733367..99733388, +
8.37e-25FFCP PHASE2:Hg19::chr19:10946872..10946894,-#_be4a6c46ff873444e2130f374769f6c8p1@TMED1
8.37e-25FFCP PHASE1:Hg19::chr19:10946872..10946894,-#_be4a6c46ff873444e2130f374769f6c8p1@TMED1
8.8e-25FFCP PHASE2:Mm9::chr16:37580298..37580310,+#_d6d5abee826806c96fcdd5f8a6ed4e4cp3@Hgd
8.8e-25FFCP PHASE1:Mm9::chr16:37580298..37580310,+#_d6d5abee826806c96fcdd5f8a6ed4e4cp3@Hgd
1.03e-24FFCP PHASE1:Mm9::chr13:58224772..58224789,-#_7854c70e2228197be26bc24bbd0241abp@chr13:58224772..58224789, -
1.03e-24FFCP PHASE2:Mm9::chr13:58224772..58224789,-#_7854c70e2228197be26bc24bbd0241abp@chr13:58224772..58224789, -
1.13e-24FFCP PHASE1:Hg19::chr8:22446763..22446862,+#_cad3ddafb88aec578ee14dd9ac656304p1@PDLIM2
1.13e-24FFCP PHASE2:Hg19::chr8:22446763..22446862,+#_cad3ddafb88aec578ee14dd9ac656304p1@PDLIM2
1.21e-24FFCP PHASE2:Mm9::chr6:3938967..3938987,-#_2a5c346ec05235544edafde3ab9c79f1p@chr6:3938967..3938987, -
1.21e-24FFCP PHASE1:Mm9::chr6:3938967..3938987,-#_2a5c346ec05235544edafde3ab9c79f1p@chr6:3938967..3938987, -
1.24e-24FFCP PHASE2:Mm9::chr15:9265320..9265378,+#_d8339aed22d7a1d6cae874a036b0ca2cp1@Ugt3a2
1.24e-24FFCP PHASE2:Hg19::chr9:136242956..136242976,-#_3112beda382f96f77bb3e8b2ff1b1deap2@SURF4
1.24e-24FFCP PHASE1:Hg19::chr9:136242956..136242976,-#_3112beda382f96f77bb3e8b2ff1b1deap2@SURF4
1.24e-24FFCP PHASE1:Mm9::chr15:9265320..9265378,+#_d8339aed22d7a1d6cae874a036b0ca2cp1@Ugt3a2
1.56e-24FFCP PHASE2:Hg19::chr9:35685631..35685657,+#_5bbece81ab994441e2a43be8766194e7p@chr9:35685631..35685657, +
1.56e-24FFCP PHASE1:Hg19::chr9:35685631..35685657,+#_5bbece81ab994441e2a43be8766194e7p@chr9:35685631..35685657, +
1.68e-24FFCP PHASE2:Hg19::chr1:113249734..113249762,-#_515a9a9f2e6f7999fbc91c209880b211p1@RHOC
1.68e-24FFCP PHASE1:Hg19::chr1:113249734..113249762,-#_515a9a9f2e6f7999fbc91c209880b211p1@RHOC
1.9e-24FFCP PHASE1:Hg19::chr9:35685273..35685313,+#_8b03e380303acdd15a798332e58ce962p@chr9:35685273..35685313, +
1.9e-24FFCP PHASE2:Hg19::chr9:35685273..35685313,+#_8b03e380303acdd15a798332e58ce962p@chr9:35685273..35685313, +
2.03e-24FFCP PHASE2:Hg19::chr7:128470453..128470472,+#_7a0e20e3195c2cc5075d4fa1c636b1c5p1@FLNC
2.03e-24FFCP PHASE1:Hg19::chr7:128470453..128470472,+#_7a0e20e3195c2cc5075d4fa1c636b1c5p1@FLNC
2.16e-24FFCP PHASE1:Mm9::chr12:58298249..58298262,-#_10f355208fbae908999f0c243e7cfc5cp5@Slc25a21
2.16e-24FFCP PHASE2:Mm9::chr12:58298249..58298262,-#_10f355208fbae908999f0c243e7cfc5cp5@Slc25a21
2.39e-24FFCP PHASE1:Hg19::chr11:66056596..66056622,-#_336ddf6f3df21ca82ebbdf1ba55f43d3p1@YIF1A
2.39e-24FFCP PHASE2:Hg19::chr11:66056596..66056622,-#_336ddf6f3df21ca82ebbdf1ba55f43d3p1@YIF1A
2.46e-24FFCP PHASE2:Mm9::chr1:177562272..177562282,+#_78b93cededc74ce93338f1189893c434p4@Kmo
2.46e-24FFCP PHASE1:Mm9::chr1:177562272..177562282,+#_78b93cededc74ce93338f1189893c434p4@Kmo
3.12e-24FFCP PHASE1:Mm9::chr16:23029135..23029149,-#_c54920742c8bca3ca51545497bc68155p4@Kng2
3.12e-24FFCP PHASE2:Mm9::chr16:23029135..23029149,-#_c54920742c8bca3ca51545497bc68155p4@Kng2
3.55e-24FFCP PHASE2:Hg19::chr4:39529049..39529067,-#_d099c2dcd09cec2087e53a43286719cbp1@UGDH
3.55e-24FFCP PHASE1:Hg19::chr4:39529049..39529067,-#_d099c2dcd09cec2087e53a43286719cbp1@UGDH










Property "Property value" (as page type) with input value "UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process., Property "Property value" (as page type) with input value "UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.