Personal tools

UBERON:0002329

From FANTOM5_SSTAR

Jump to: navigation, search

Name:somite
Namespace:FANTOM
Definition:"A segmental mass of mesoderm in the vertebrate embryo, occurring in pairs along the notochord and developing into muscles and vertebrae[BTO]. Portion of mesoderm distributed along the two sides of the neural tube and that will eventually become dermis (dermatome), skeletal muscle (myotome), and vertebrae (sclerotome)[WP]. In Zebrafish: Any of the approximately 45 bilaterally paired blocks of mesoderm cells, lying on either side of the notochord and neural tube, and forming sequentially starting at the head during development of the embryo. Together they give rise to the axial skeleton (from the sclerotome), associated musculature (from the myotome), and dermis (from the dermatome). // Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. <a href
Xrefs:
links:

AAO:0010569
BTO:0001558
EHDAA2:0003436
EHDAA:366
EHDAA:699
FMA:85522
GAID:1306
[ Gray19_with_color.png Gray19_with_color.png]
[ 200px-Gray19_with_color.png 200px-Gray19_with_color.png]
MAT:0000068
MESH:A.16.254.425.660.750
MIAA:0000068
ncithesaurus:Somite
TAO:0000155
VHOG:0000191
XAO:0000058

ZFA:0000155
Synonyms: "epithelial somite" RELATED [UBERONREF:0000002]
"mesodermal cluster" EXACT [GO:0001756]
"somites" RELATED PLURAL []
"somitic mesoderm" RELATED []
"somitus" RELATED LATIN [Wikipedia:Somite]
Comments:Editor notes: currently classified as an epithelial vesicle, consistent with EHDAA2 and UBERONREF:0000002. Consider making "somitic mesoderm" a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk // When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
Alt_id: UBERON:FMA_85522-MIAA_0000068-XAO_0000058-ZFA_0000155
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:0005423(developing anatomical structure),UBERON:0007503(epithelial vesicle),UBERON:0012275(meso-epithelium)
develops_from:UBERON:0003059(presomitic mesoderm)



Children

develops from:UBERON:0003082 (myotome),UBERON:0003089 (sclerotome),UBERON:0004016 (dermatome),UBERON:0004290 (dermomyotome)
part of:FF:0000226 (chicken embryo whole body day1 HH7 1-3 somites),FF:0000227 (chicken embryo whole body day1 HH7 2-3 somites)

Ontology Tree: Loaded from BioPortal


FF samples
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:0002329 (somite), sorted by p-values
Analyst: Hideya Kawaji

link to source dataset
human : data
mouse : data


P-valueFFCPShort description
5.24e-58FFCP PHASE2:Mm9::chrX:160838683..160838694,+#_8d7fbf366c0b7d7622c6a385f39e419dp@chrX:160838683..160838694, +
5.24e-58FFCP PHASE1:Mm9::chrX:160838683..160838694,+#_8d7fbf366c0b7d7622c6a385f39e419dp@chrX:160838683..160838694, +
5.11e-50FFCP PHASE1:Mm9::chrX:65748600..65748616,+#_ad7de030602e659e6670afb0e206724cp@chrX:65748600..65748616, +
5.11e-50FFCP PHASE2:Mm9::chrX:65748600..65748616,+#_ad7de030602e659e6670afb0e206724cp@chrX:65748600..65748616, +
5.11e-50FFCP PHASE1:Mm9::chr12:105433069..105433075,-#_ad7de030602e659e6670afb0e206724cp@chr12:105433069..105433075, -
5.11e-50FFCP PHASE2:Mm9::chr12:105433069..105433075,-#_ad7de030602e659e6670afb0e206724cp@chr12:105433069..105433075, -
1.47e-48FFCP PHASE2:Mm9::chrX:160838787..160838800,+#_17e5945434357ee6519245a1e6e2c703p@chrX:160838787..160838800, +
1.47e-48FFCP PHASE1:Mm9::chrX:160838787..160838800,+#_17e5945434357ee6519245a1e6e2c703p@chrX:160838787..160838800, +
1.58e-44FFCP PHASE1:Hg19::chr10:49813077..49813087,-#_82df0112630a26a80032e9da8afbadb6p8@ARHGAP22
1.58e-44FFCP PHASE2:Hg19::chr10:49813077..49813087,-#_82df0112630a26a80032e9da8afbadb6p8@ARHGAP22
8.42e-44FFCP PHASE2:Mm9::chr11:81849982..81850000,+#_0df4e201676a5363253cef527811eb2cp@chr11:81849982..81850000, +
8.42e-44FFCP PHASE1:Mm9::chr11:81849982..81850000,+#_0df4e201676a5363253cef527811eb2cp@chr11:81849982..81850000, +
9.2e-41FFCP PHASE2:Hg19::chr6:53359400..53359406,+#_e83a70b101c1a9efccee38e5733b6364p@chr6:53359400..53359406, +
9.2e-41FFCP PHASE1:Hg19::chr6:53359400..53359406,+#_e83a70b101c1a9efccee38e5733b6364+, p@chr6:53359400..53359406
1.15e-40FFCP PHASE1:Mm9::chr17:14813242..14813246,-#_510087d49285d4fe4c987cc083584e67p@chr17:14813242..14813246, -
1.15e-40FFCP PHASE2:Mm9::chr17:14813242..14813246,-#_510087d49285d4fe4c987cc083584e67p@chr17:14813242..14813246, -
2.26e-39FFCP PHASE2:Hg19::chr10:49813051..49813064,-#_f85682b92040c00d57025e257e5add09p4@ARHGAP22
2.26e-39FFCP PHASE1:Hg19::chr10:49813051..49813064,-#_f85682b92040c00d57025e257e5add09p4@ARHGAP22
2.88e-39FFCP PHASE2:Hg19::chr9:35685631..35685657,+#_d51e437ad7d1610bf1a4b347ef57196bp@chr9:35685631..35685657, +
2.88e-39FFCP PHASE1:Hg19::chr9:35685631..35685657,+#_d51e437ad7d1610bf1a4b347ef57196bp@chr9:35685631..35685657, +
3.7e-39FFCP PHASE2:Mm9::chr1:127573795..127573810,+#_5319746916cfef281573dddfab755315p4@Gpr39
3.7e-39FFCP PHASE1:Mm9::chr1:127573795..127573810,+#_5319746916cfef281573dddfab755315p4@Gpr39
3.75e-39FFCP PHASE2:Mm9::chrX:160823859..160823870,+#_251f24ab76de1d11be3a7e9df3fc5032p@chrX:160823859..160823870, +
3.75e-39FFCP PHASE2:Mm9::chrX:160840025..160840037,+#_251f24ab76de1d11be3a7e9df3fc5032p@chrX:160840025..160840037, +
3.75e-39FFCP PHASE2:Mm9::chrX:160840048..160840057,+#_251f24ab76de1d11be3a7e9df3fc5032p@chrX:160840048..160840057, +
3.75e-39FFCP PHASE1:Mm9::chrX:160823859..160823870,+#_251f24ab76de1d11be3a7e9df3fc5032p@chrX:160823859..160823870, +
3.75e-39FFCP PHASE1:Mm9::chrX:160840025..160840037,+#_251f24ab76de1d11be3a7e9df3fc5032p@chrX:160840025..160840037, +
3.75e-39FFCP PHASE1:Mm9::chrX:160840048..160840057,+#_251f24ab76de1d11be3a7e9df3fc5032p@chrX:160840048..160840057, +
1.14e-38FFCP PHASE2:Hg19::chr6:148593425..148593498,+#_de2bec7ff2c5ff93b2ac81f7c2ea9cf3p2@SASH1
1.14e-38FFCP PHASE1:Hg19::chr6:148593425..148593498,+#_de2bec7ff2c5ff93b2ac81f7c2ea9cf3p2@SASH1
1.34e-36FFCP PHASE1:Hg19::chr10:49813013..49813032,-#_5eb9edbe5512000df56a99b717e2384ep3@ARHGAP22
1.34e-36FFCP PHASE2:Hg19::chr10:49813013..49813032,-#_5eb9edbe5512000df56a99b717e2384ep3@ARHGAP22
1.46e-35FFCP PHASE1:Hg19::chr19:50031567..50031632,+#_e1d4094095cedc3d8ae347add85dbdd0p2@RCN3
1.46e-35FFCP PHASE2:Hg19::chr19:50031567..50031632,+#_e1d4094095cedc3d8ae347add85dbdd0p2@RCN3
3.31e-35FFCP PHASE2:Mm9::chr3:79689074..79689090,+#_5672f3cb1383dc64c1ea17968a314a60p11@Fam198b
3.31e-35FFCP PHASE1:Mm9::chr3:79689074..79689090,+#_5672f3cb1383dc64c1ea17968a314a60p11@Fam198b
3.69e-35FFCP PHASE1:Mm9::chr1:127574253..127574264,+#_55f9dce0cbdcaeec2b7eeb1d1ad9bee2p@chr1:127574253..127574264, +
3.69e-35FFCP PHASE2:Mm9::chr1:127574253..127574264,+#_55f9dce0cbdcaeec2b7eeb1d1ad9bee2p@chr1:127574253..127574264, +
5.09e-35FFCP PHASE2:Mm9::chr1:127573733..127573745,+#_88f84c983bb641dda4464496dfb5ce1ap7@Gpr39
5.09e-35FFCP PHASE1:Mm9::chr1:127573733..127573745,+#_88f84c983bb641dda4464496dfb5ce1ap7@Gpr39
5.98e-35FFCP PHASE1:Mm9::chr1:127573690..127573699,+#_bc2dd3d1dc18c514c2c17d8ca874d36ep11@Gpr39
5.98e-35FFCP PHASE2:Mm9::chr1:127573690..127573699,+#_bc2dd3d1dc18c514c2c17d8ca874d36ep11@Gpr39
7.03e-35FFCP PHASE1:Mm9::chrX:160839768..160839780,+#_641e6e29543c48fa5a5e9179e3b40dc6p@chrX:160839768..160839780, +
7.03e-35FFCP PHASE2:Mm9::chrX:160839768..160839780,+#_641e6e29543c48fa5a5e9179e3b40dc6p@chrX:160839768..160839780, +
9.95e-35FFCP PHASE1:Hg19::chr9:35685445..35685517,+#_098ac8bcc815e2e18b63c37d16875e4ap@chr9:35685445..35685517, +
9.95e-35FFCP PHASE2:Hg19::chr9:35685445..35685517,+#_098ac8bcc815e2e18b63c37d16875e4ap@chr9:35685445..35685517, +
1.33e-34FFCP PHASE1:Mm9::chr1:127573462..127573472,+#_a9b6b0118a7b44e2efb15bd26e87af23p8@Gpr39
1.33e-34FFCP PHASE2:Mm9::chr1:127573462..127573472,+#_a9b6b0118a7b44e2efb15bd26e87af23p8@Gpr39
1.89e-34FFCP PHASE1:Hg19::chr9:35684475..35684520,+#_439c3e3d2505f0c9ea1deb4cd589b0e7p@chr9:35684475..35684520, +
1.89e-34FFCP PHASE2:Hg19::chr9:35684475..35684520,+#_439c3e3d2505f0c9ea1deb4cd589b0e7p@chr9:35684475..35684520, +
4.48e-34FFCP PHASE1:Hg19::chr14:94595800..94595811,-#_0072eeb789af01f589db066694702f19p3@IFI27L2
4.48e-34FFCP PHASE2:Hg19::chr14:94595800..94595811,-#_0072eeb789af01f589db066694702f19p3@IFI27L2
5.0e-34FFCP PHASE1:Hg19::chr7:102553470..102553487,+#_55b43bf77e1fabcb839d1a821dbf4b45p2@LRRC17
5.0e-34FFCP PHASE2:Hg19::chr7:102553470..102553487,+#_55b43bf77e1fabcb839d1a821dbf4b45p2@LRRC17
2.06e-33FFCP PHASE1:Hg19::chr9:35689148..35689192,+#_4e0701c10d46047e544830f6aae50fa4p@chr9:35689148..35689192, +
2.06e-33FFCP PHASE2:Hg19::chr9:35689148..35689192,+#_4e0701c10d46047e544830f6aae50fa4p@chr9:35689148..35689192, +
7.56e-33FFCP PHASE2:Hg19::chr7:102553430..102553456,+#_aa5283807ab111003111e205ce78dd75p1@LRRC17
7.56e-33FFCP PHASE1:Hg19::chr7:102553430..102553456,+#_aa5283807ab111003111e205ce78dd75p1@LRRC17
1.21e-32FFCP PHASE2:Hg19::chr21:47518695..47518709,+#_7ab05bd9f6f364bd6a860c96c66f57bep6@COL6A2
1.21e-32FFCP PHASE1:Hg19::chr21:47518695..47518709,+#_7ab05bd9f6f364bd6a860c96c66f57bep6@COL6A2
2.74e-32FFCP PHASE1:Hg19::chr21:47518637..47518688,+#_c9cd3137477bf8d3edf76fd55c1b6c7bp2@COL6A2
2.74e-32FFCP PHASE2:Hg19::chr21:47518637..47518688,+#_c9cd3137477bf8d3edf76fd55c1b6c7bp2@COL6A2
3.94e-32FFCP PHASE2:Mm9::chr7:96658543..96658553,-#_a6e7e74e4c73bb4a8b5d314a852d9e8fp@chr7:96658543..96658553, -
3.94e-32FFCP PHASE1:Mm9::chr7:96658543..96658553,-#_a6e7e74e4c73bb4a8b5d314a852d9e8fp@chr7:96658543..96658553, -
5.83e-32FFCP PHASE2:Hg19::chr4:74703497..74703511,+#_e4e0e9e497230735d3b0a1b44eecd92ap@chr4:74703497..74703511, +
5.83e-32FFCP PHASE1:Hg19::chr4:74703497..74703511,+#_e4e0e9e497230735d3b0a1b44eecd92ap@chr4:74703497..74703511, +
9.0e-32FFCP PHASE2:Hg19::chr2:134548872..134548879,-#_f07d4ec536b6adb9a7025324cec8e2b2p@chr2:134548872..134548879, -
9.0e-32FFCP PHASE1:Hg19::chr2:134548872..134548879,-#_f07d4ec536b6adb9a7025324cec8e2b2p@chr2:134548872..134548879, -
9.7e-32FFCP PHASE1:Hg19::chr9:35685273..35685313,+#_5947da35b0fbd3b5a842914c426d79d8p@chr9:35685273..35685313, +
9.7e-32FFCP PHASE2:Hg19::chr9:35685273..35685313,+#_5947da35b0fbd3b5a842914c426d79d8p@chr9:35685273..35685313, +
1.33e-31FFCP PHASE2:Mm9::chr7:91081998..91082010,-#_b43ebe74a85e9e21b2a4e229dcc358a3p@chr7:91081998..91082010, -
1.33e-31FFCP PHASE1:Mm9::chr5:30339923..30339935,+#_b43ebe74a85e9e21b2a4e229dcc358a3p2@Il6
1.33e-31FFCP PHASE1:Mm9::chr7:91081998..91082010,-#_b43ebe74a85e9e21b2a4e229dcc358a3p@chr7:91081998..91082010, -
1.33e-31FFCP PHASE2:Mm9::chr5:30339923..30339935,+#_b43ebe74a85e9e21b2a4e229dcc358a3p2@Il6
1.59e-31FFCP PHASE1:Mm9::chr10:67598037..67598049,-#_d34c6228e9a2ae72a442c6041f803ab0p@chr10:67598037..67598049, -
1.59e-31FFCP PHASE2:Mm9::chr10:67598037..67598049,-#_d34c6228e9a2ae72a442c6041f803ab0p@chr10:67598037..67598049, -
2.72e-31FFCP PHASE2:Mm9::chr2:65009852..65009866,-#_91476aae558fb97cdc58e1ad3dff05f0p@chr2:65009852..65009866, -
2.72e-31FFCP PHASE1:Mm9::chr2:65009852..65009866,-#_91476aae558fb97cdc58e1ad3dff05f0p@chr2:65009852..65009866, -
2.8e-31FFCP PHASE1:Mm9::chr18:52678391..52678395,-#_05677ff3c00ad0d4c3fe915138f5e5f2p@chr18:52678391..52678395, -
2.8e-31FFCP PHASE2:Mm9::chr18:52678391..52678395,-#_05677ff3c00ad0d4c3fe915138f5e5f2p@chr18:52678391..52678395, -
7.65e-31FFCP PHASE1:Mm9::chr6:91222095..91222107,+#_397df25ef20a6ef22f8b024f9182b549p@chr6:91222095..91222107, +
7.65e-31FFCP PHASE2:Mm9::chr6:91222095..91222107,+#_397df25ef20a6ef22f8b024f9182b549p@chr6:91222095..91222107, +
9.72e-31FFCP PHASE2:Hg19::chr1:79472477..79472510,-#_1c636a0c7fc3745c8e1d13ab22629a62p2@ELTD1
9.72e-31FFCP PHASE1:Hg19::chr1:79472477..79472510,-#_1c636a0c7fc3745c8e1d13ab22629a62p2@ELTD1
1.01e-30FFCP PHASE2:Hg19::chr7:100773764..100773799,-#_dafc4b4414a696ce4e286e36b5994a0fp@chr7:100773764..100773799, -
1.01e-30FFCP PHASE2:Mm9::chr5:114822634..114822665,-#_3dbaaf9aa2c8d5f90d54f174d652c6bap9@Kctd10
1.01e-30FFCP PHASE1:Hg19::chr7:100773764..100773799,-#_dafc4b4414a696ce4e286e36b5994a0fp@chr7:100773764..100773799, -
1.01e-30FFCP PHASE1:Mm9::chr5:114822634..114822665,-#_3dbaaf9aa2c8d5f90d54f174d652c6bap9@Kctd10
1.17e-30FFCP PHASE1:Mm9::chr1:127573773..127573786,+#_c410863f2a736fb680e40085799be469p6@Gpr39
1.17e-30FFCP PHASE2:Mm9::chr1:127573773..127573786,+#_c410863f2a736fb680e40085799be469p6@Gpr39
1.26e-30FFCP PHASE2:Hg19::chr12:53491743..53491754,+#_e80ffea9e1262d3c824ea97a596586aep1@AK074416
1.26e-30FFCP PHASE1:Hg19::chr12:53491743..53491754,+#_e80ffea9e1262d3c824ea97a596586aep1@AK074416
1.4e-30FFCP PHASE1:Hg19::chr7:93516035..93516056,+#_9dab122ec2675a2748aabc025b6e119ep1@CU675118
1.4e-30FFCP PHASE2:Hg19::chr7:93516035..93516056,+#_9dab122ec2675a2748aabc025b6e119ep1@CU675118
1.8e-30FFCP PHASE2:Hg19::chr21:47532318..47532355,+#_1f9b1e0635bb1449e83ade5e5523c338p8@COL6A2
1.8e-30FFCP PHASE1:Hg19::chr21:47532318..47532355,+#_1f9b1e0635bb1449e83ade5e5523c338p8@COL6A2
2.01e-30FFCP PHASE1:Hg19::chr2:33359687..33359717,+#_b8994909235a9bcd121b08df619732c4p2@LTBP1
2.01e-30FFCP PHASE2:Hg19::chr2:33359687..33359717,+#_b8994909235a9bcd121b08df619732c4p2@LTBP1
3.87e-30FFCP PHASE2:Hg19::chr21:47542827..47542859,-#_4e873785dd3c87663e99005ba19c6827-, p@chr21:47542827..47542859
3.87e-30FFCP PHASE1:Hg19::chr21:47542827..47542859,-#_4e873785dd3c87663e99005ba19c6827p@chr21:47542827..47542859, -










Property "Property value" (as page type) with input value "UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" 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 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. 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:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[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:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" 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:0000002 "relationship type change: part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.