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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

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.



link to ontology dataset


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


FF samples

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
Analyst: Hideya Kawaji



link to source dataset
human : data

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 PHASE1:Hg19::chr8:30242040..30242045,+#_6ca15889149aa8712435b6b0d96b8530p2@RBPMS
1.91e-30FFCP PHASE2:Hg19::chr8:30242040..30242045,+#_6ca15889149aa8712435b6b0d96b8530p2@RBPMS
2.99e-28FFCP PHASE2:Hg19::chr8:30242048..30242064,+#_8f05d5693ec71cdc44b81f1165c554bcp1@RBPMS
2.99e-28FFCP PHASE1:Hg19::chr8:30242048..30242064,+#_8f05d5693ec71cdc44b81f1165c554bcp1@RBPMS
5.64e-28FFCP PHASE1:Hg19::chr8:30241934..30241945,+#_4bbcc577702ee1b5f3e91f7444c57472p3@RBPMS
5.64e-28FFCP PHASE2:Hg19::chr8:30241934..30241945,+#_4bbcc577702ee1b5f3e91f7444c57472p3@RBPMS
6.23e-28FFCP PHASE2:Mm9::chr6:34129226..34129246,+#_42c98e2c8e8ce253758cd386bbf5cba4p2@ENSMUST00000145644
6.23e-28FFCP PHASE1:Mm9::chr6:34129226..34129246,+#_42c98e2c8e8ce253758cd386bbf5cba4p2@ENSMUST00000145644
6.8e-28FFCP PHASE2:Mm9::chr8:73247943..73247958,+#_323160c25c633476891171e1a8dd3559p3@Pde4c
6.8e-28FFCP PHASE1:Mm9::chr8:73247943..73247958,+#_323160c25c633476891171e1a8dd3559p3@Pde4c
2.88e-27FFCP PHASE2:Hg19::chr11:114167164..114167190,+#_8e1c43b848111e2eefb76f23353895e7p2@NNMT
2.88e-27FFCP PHASE1: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 PHASE1:Hg19::chr19:48894762..48894830,-#_a00594996c7d7eeb847c486a7553c907p1@KDELR1
5.08e-27FFCP PHASE2:Hg19::chr19:48894762..48894830,-#_a00594996c7d7eeb847c486a7553c907p1@KDELR1
1.09e-26FFCP PHASE1:Mm9::chr11:60622345..60622377,-#_efe0067227b485d98c069a964c81886ap@chr11:60622345..60622377, -
1.09e-26FFCP PHASE2:Mm9::chr11:60622345..60622377,-#_efe0067227b485d98c069a964c81886a-, p@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 PHASE2:Mm9::chr19:12707997..12708015,+#_55b8bcff8242360f3dec1649c419ed3fp1@Glyat
2.8e-26FFCP PHASE1:Mm9::chr19:12707997..12708015,+#_55b8bcff8242360f3dec1649c419ed3fp1@Glyat
3.19e-26FFCP PHASE1:Mm9::chr13:23931270..23931311,+#_ea04df79573d5bd6753a0164d9906a95p2@Slc17a3
3.19e-26FFCP PHASE2:Mm9::chr13:23931270..23931311,+#_ea04df79573d5bd6753a0164d9906a95p2@Slc17a3
3.4e-26FFCP PHASE2:Mm9::chr16:37621995..37622022,-#_c50f994e9b930db751a30e2a608e8cd4p@chr16:37621995..37622022, -
3.4e-26FFCP PHASE1:Mm9::chr16:37621995..37622022,-#_c50f994e9b930db751a30e2a608e8cd4p@chr16:37621995..37622022, -
4.15e-26FFCP PHASE1:Hg19::chr11:114167202..114167221,+#_7ee61ef3bc6592109c1dd41f68327426p3@NNMT
4.15e-26FFCP PHASE2:Hg19::chr11:114167202..114167221,+#_7ee61ef3bc6592109c1dd41f68327426p3@NNMT
6.21e-26FFCP PHASE1:Mm9::chr13:23931467..23931489,+#_1f969e856e94e4d435f617252d0f448ep3@Slc17a3
6.21e-26FFCP PHASE2:Mm9::chr13:23931467..23931489,+#_1f969e856e94e4d435f617252d0f448ep3@Slc17a3
7.91e-26FFCP PHASE1:Mm9::chr4:96330769..96330789,-#_c630ab23f37af7e383a05d2311ada4f8p2@Cyp2j5
7.91e-26FFCP PHASE2:Mm9::chr4:96330769..96330789,-#_c630ab23f37af7e383a05d2311ada4f8p2@Cyp2j5
1.05e-25FFCP PHASE1:Mm9::chr1:142079981..142079992,-#_6d2b88f0f6a3814ea50e0fbddd3acc3dp3@Cfh
1.05e-25FFCP PHASE2: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 PHASE1:Mm9::chr16:37580223..37580237,+#_f2b2fc848a8e355e4e2650aae02f918bp4@Hgd
1.32e-25FFCP PHASE2: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 PHASE1:Mm9::chr4:95246137..95246153,+#_b135e1781ceca25c8cbabe8d0e26b5cfp3@Fggy
1.79e-25FFCP PHASE2: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 PHASE2:Hg19::chr14:35183837..35183867,-#_933eeb3fb718ced420947367b4de589ap2@CFL2
2.31e-25FFCP PHASE1:Hg19::chr14:35183837..35183867,-#_933eeb3fb718ced420947367b4de589ap2@CFL2
2.74e-25FFCP PHASE2:Hg19::chr5:148521286..148521377,+#_b546599d4402a5a0496ff15857a92671p2@ABLIM3
2.74e-25FFCP PHASE1:Hg19::chr5:148521286..148521377,+#_b546599d4402a5a0496ff15857a92671p2@ABLIM3
2.77e-25FFCP PHASE1:Mm9::chr9:44609886..44609901,-#_7e01e16957a28223677915ebd471be08p@chr9:44609886..44609901, -
2.77e-25FFCP PHASE2:Mm9::chr9:44609886..44609901,-#_7e01e16957a28223677915ebd471be08p@chr9:44609886..44609901, -
4.16e-25FFCP PHASE2:Mm9::chr4:150283537..150283568,-#_af0ff882a507956c3703aa0aec62644ap5@Park7
4.16e-25FFCP PHASE1:Mm9::chr4:150283537..150283568,-#_af0ff882a507956c3703aa0aec62644ap5@Park7
4.54e-25FFCP PHASE1:Mm9::chr12:58298278..58298292,-#_493f1ab84007bcc2b4709f34451bf9ebp4@Slc25a21
4.54e-25FFCP PHASE2: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 PHASE2:Mm9::chr15:99733367..99733388,+#_4679f11546fc00992f2359e54e12448fp@chr15:99733367..99733388, +
5.09e-25FFCP PHASE1: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 PHASE2:Hg19::chr8:22446763..22446862,+#_cad3ddafb88aec578ee14dd9ac656304p1@PDLIM2
1.13e-24FFCP PHASE1:Hg19::chr8:22446763..22446862,+#_cad3ddafb88aec578ee14dd9ac656304p1@PDLIM2
1.21e-24FFCP PHASE1:Mm9::chr6:3938967..3938987,-#_2a5c346ec05235544edafde3ab9c79f1p@chr6:3938967..3938987, -
1.21e-24FFCP PHASE2:Mm9::chr6:3938967..3938987,-#_2a5c346ec05235544edafde3ab9c79f1p@chr6:3938967..3938987, -
1.24e-24FFCP PHASE1:Hg19::chr9:136242956..136242976,-#_3112beda382f96f77bb3e8b2ff1b1deap2@SURF4
1.24e-24FFCP PHASE2:Hg19::chr9:136242956..136242976,-#_3112beda382f96f77bb3e8b2ff1b1deap2@SURF4
1.24e-24FFCP PHASE2:Mm9::chr15:9265320..9265378,+#_d8339aed22d7a1d6cae874a036b0ca2cp1@Ugt3a2
1.24e-24FFCP PHASE1:Mm9::chr15:9265320..9265378,+#_d8339aed22d7a1d6cae874a036b0ca2cp1@Ugt3a2
1.56e-24FFCP PHASE1:Hg19::chr9:35685631..35685657,+#_5bbece81ab994441e2a43be8766194e7p@chr9:35685631..35685657, +
1.56e-24FFCP PHASE2: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 PHASE2:Hg19::chr9:35685273..35685313,+#_8b03e380303acdd15a798332e58ce962p@chr9:35685273..35685313, +
1.9e-24FFCP PHASE1: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 PHASE1:Hg19::chr4:39529049..39529067,-#_d099c2dcd09cec2087e53a43286719cbp1@UGDH
3.55e-24FFCP PHASE2: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.