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|located_in=
|located_in=
|name=embryo
|name=embryo
|namespace=
|namespace=FANTOM
|obo_creation_date=
|obo_creation_date=
|part_of=
|part_of=

Latest revision as of 17:10, 12 September 2014

Name:embryo
Namespace:FANTOM
Definition:"Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [BTO:0000379, FB:FBrf0039741, FB:FBrf0041814, GO:0009790, Wikipedia:Embryo]
Xrefs:
links:

AAO:0011035
AEO:0000169
BILA:0000056
BTO:0000379
EFO:0001367
EHDAA2:0003236
EHDAA:38
EMAPA:16039
FBbt:00000052
FMA:69068
GAID:963
[1]
MAT:0000226
MESH:A.16.254
MIAA:0000019
ncithesaurus:Embryo
OGEM:000001
OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA
SCTID:57991002
XAO:0000113

ZFA:0000103
Synonyms: "developing organism" RELATED [BILA:0000056]
"developmental tissue" RELATED []
"embryonic organism" EXACT [BILA:0000056]
Comments:Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
Alt_id: UBERON:FBbt_00000052-FMA_69068-MIAA_0000019-XAO_0000113
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:0000468(multi-cellular organism)



Children

is a:UBERON:0000085 (morula),UBERON:0000307 (blastula),UBERON:0000323 (late embryo),UBERON:0004734 (gastrula),UBERON:0007010 (cleaving embryo),FF:10004-101A9 (chicken embryo whole body, day10 (HH37)),FF:10590-108D5 (testicular germ cell embryonal carcinoma cell line:NEC8),FF:10591-108D6 (testicular germ cell embryonal carcinoma cell line:NEC14),FF:10593-108D8 (testicular germ cell embryonal carcinoma cell line:NEC15),FF:10786-110H3 (testicular germ cell embryonal carcinoma cell line:ITO-II),FF:11949-126B5 (hematopoietic stem cell, aorta-gonad-mesonephros (AGM) region derived, embryo E10.5),FF:11956-126C3 (hematopoietic stem cell, bone marrow derived, embryo E19.5)
derives from:FF:0000999 (fetal tissue sample),FF:0100669 (embryonic cell line sample)
part of:UBERON:0000076 (external ectoderm),UBERON:0000087 (inner cell mass),UBERON:0000163 (embryonic cloaca),FF:0000217 (chicken whole embryo),FF:0000218 (chicken embryo extraembryonic tissue day7 HH32),FF:0000219 (chicken embryo extraembryonic tissue day15 HH41),FF:0000220 (chicken embryo whole body 1.5 hours HH1),FF:0000221 (chicken embryo whole body 14 hours HH3),FF:0000222 (chicken embryo whole body 18 hours HH4),FF:0000223 (chicken embryo whole body 22 hours HH5-6),FF:0000224 (chicken embryo whole body 5.5 hours HH1),FF:0000225 (chicken embryo whole body 6 hours HH1-2),FF:0000226 (chicken embryo whole body day1 HH7 1-3 somites),FF:0000227 (chicken embryo whole body day1 HH7 2-3 somites),FF:0000228 (chicken embryo whole body day1.5 HH10),FF:0000230 (chicken embryo whole body day1.5 HH11-12),FF:0000231 (chicken embryo whole body day 15 HH11-12),FF:0000232 (chicken embryo whole body day2 HH13),FF:0000233 (chicken embryo whole body day2 HH14),FF:0000234 (chicken embryo whole body day2.5 HH17),FF:0000235 (chicken embryo whole body day20 HH45),FF:0000236 (chicken embryo whole body day3 HH19),FF:0000237 (chicken embryo whole body day3 HH20),FF:0000238 (chicken embryo whole body day4 HH23),FF:0000239 (chicken embryo whole body day5 HH25-27),FF:0000240 (chicken embryo whole body day5 HH26-27),FF:0000241 (chicken embryo whole body day7 HH32),UBERON:0000923 (germ layer),UBERON:0001049 (neural tube),UBERON:0002050 (embryonic structure),UBERON:0002062 (endocardial cushion),CL:0002352 (gestational hematopoietic stem cell),UBERON:0003050 (olfactory placode),UBERON:0003051 (ear vesicle),UBERON:0003061 (blood island),UBERON:0003063 (prechordal plate),UBERON:0003064 (intermediate mesoderm),UBERON:0003068 (axial mesoderm),UBERON:0003075 (neural plate),UBERON:0003077 (paraxial mesoderm),UBERON:0003080 (anterior neural tube),UBERON:0003220 (metanephric mesenchyme),UBERON:0003285 (limb of embryo),UBERON:0003820 (prostate bud),UBERON:0003890 (Mullerian duct),UBERON:0003921 (pancreas primordium),UBERON:0004061 (neural tube mantle layer),UBERON:0004117 (pharyngeal pouch),UBERON:0004139 (cardiogenic plate),UBERON:0004141 (heart tube)... further results

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:0000922 (embryo), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

P-valueFFCPShort description
1.01e-31FFCP PHASE2:Hg19::chr13:45010939..45011033,-#_9c78662fb528cda5f1036a92c0bca034p1@TSC22D1
1.01e-31FFCP PHASE1:Hg19::chr13:45010939..45011033,-#_9c78662fb528cda5f1036a92c0bca034p1@TSC22D1
7.11e-30FFCP PHASE2:Hg19::chr7:111846435..111846471,-#_aca40c43c23c0cfef683eb40c86d0e99p1@DOCK4
7.11e-30FFCP PHASE1:Hg19::chr7:111846435..111846471,-#_aca40c43c23c0cfef683eb40c86d0e99p1@DOCK4
3.46e-28FFCP PHASE2:Hg19::chr20:23618584..23618603,-#_31f75abdae37ef708d3a59467dbf0adbp1@CST3
3.46e-28FFCP PHASE1:Hg19::chr20:23618584..23618603,-#_31f75abdae37ef708d3a59467dbf0adbp1@CST3
1.55e-27FFCP PHASE1:Hg19::chr2:24272576..24272619,+#_c912edfb1ca9b101b0eac4b6ffad850fp1@FKBP1B
1.55e-27FFCP PHASE2:Hg19::chr2:24272576..24272619,+#_c912edfb1ca9b101b0eac4b6ffad850fp1@FKBP1B
5.56e-27FFCP PHASE1:Hg19::chr8:30670289..30670354,-#_79e5544388b175e0d2076c9eb74dc973p1@PPP2CB
5.56e-27FFCP PHASE2:Hg19::chr8:30670289..30670354,-#_79e5544388b175e0d2076c9eb74dc973p1@PPP2CB
1.68e-26FFCP PHASE2:Hg19::chr2:153191678..153191697,+#_4d5698b19b858300f69bc4098ba3eb70p1@FMNL2
1.68e-26FFCP PHASE1:Hg19::chr2:153191678..153191697,+#_4d5698b19b858300f69bc4098ba3eb70p1@FMNL2
2.34e-26FFCP PHASE2:Hg19::chr13:77460532..77460548,-#_233efb8da76b7cbaf4b984c173b4845ap1@KCTD12
2.34e-26FFCP PHASE1:Hg19::chr13:77460532..77460548,-#_233efb8da76b7cbaf4b984c173b4845ap1@KCTD12
8.69e-26FFCP PHASE1:Hg19::chr12:112204714..112204781,+#_b67b383165c9deac0e817063f9099e40p1@ALDH2
8.69e-26FFCP PHASE2:Hg19::chr12:112204714..112204781,+#_b67b383165c9deac0e817063f9099e40p1@ALDH2
1.57e-25FFCP PHASE1:Hg19::chr8:28559004..28559039,+#_c7e9ac2cc960d45e581e70ed7b208364p1@EXTL3
1.57e-25FFCP PHASE2:Hg19::chr8:28559004..28559039,+#_c7e9ac2cc960d45e581e70ed7b208364p1@EXTL3
2.9e-25FFCP PHASE1:Hg19::chr11:1330834..1330875,-#_614e9af94857dcfe2c004b9622eb37e8p1@TOLLIP
2.9e-25FFCP PHASE2:Hg19::chr11:1330834..1330875,-#_614e9af94857dcfe2c004b9622eb37e8p1@TOLLIP
3.28e-25FFCP PHASE2:Hg19::chr16:4852616..4852679,-#_58d0770155da8ebde36e058e11bea454p1@ROGDI
3.28e-25FFCP PHASE1:Hg19::chr16:4852616..4852679,-#_58d0770155da8ebde36e058e11bea454p1@ROGDI
3.33e-25FFCP PHASE2:Hg19::chr10:30025922..30025958,-#_8c1220506dcf3937b2d3227d50e985bap3@SVIL
3.33e-25FFCP PHASE1:Hg19::chr10:30025922..30025958,-#_8c1220506dcf3937b2d3227d50e985bap3@SVIL
5.9e-25FFCP PHASE2:Hg19::chr4:85887789..85887862,-#_c316ccdeeee7a38aaffdab21ae7df24fp1@WDFY3
5.9e-25FFCP PHASE1:Hg19::chr4:85887789..85887862,-#_c316ccdeeee7a38aaffdab21ae7df24fp1@WDFY3
7.48e-25FFCP PHASE1:Hg19::chr17:1466030..1466129,-#_6911c154dafee9b62bd197db61d90940p1@PITPNA
7.48e-25FFCP PHASE2:Hg19::chr17:1466030..1466129,-#_6911c154dafee9b62bd197db61d90940p1@PITPNA
1.07e-24FFCP PHASE2:Hg19::chr15:90456156..90456198,-#_7de6cc1edaac68faa763ff9bf4852a7dp1@C15orf38
1.07e-24FFCP PHASE1:Hg19::chr15:90456156..90456198,-#_7de6cc1edaac68faa763ff9bf4852a7dp1@C15orf38
2.21e-24FFCP PHASE2:Hg19::chr2:127864608..127864688,-#_b052eadc1fb285e9d912b5252cb46246p1@BIN1
2.21e-24FFCP PHASE1:Hg19::chr2:127864608..127864688,-#_b052eadc1fb285e9d912b5252cb46246p1@BIN1
2.22e-24FFCP PHASE1:Hg19::chr2:230135937..230136016,-#_e3e4b3ea7b882aa605a42b7294a79822p1@PID1
2.22e-24FFCP PHASE2:Hg19::chr2:230135937..230136016,-#_e3e4b3ea7b882aa605a42b7294a79822p1@PID1
3.57e-24FFCP PHASE1:Hg19::chr19:40871734..40871809,+#_e4123f5eb23e83e9e64d3d62ae0f27d9p1@PLD3
3.57e-24FFCP PHASE2:Hg19::chr19:40871734..40871809,+#_e4123f5eb23e83e9e64d3d62ae0f27d9p1@PLD3
5.03e-24FFCP PHASE1:Hg19::chr17:7492684..7492778,-#_326d02110ebc57b5997bd768a1a0b4dcp2@SOX15
5.03e-24FFCP PHASE2:Hg19::chr17:7492684..7492778,-#_326d02110ebc57b5997bd768a1a0b4dcp2@SOX15
8.56e-24FFCP PHASE1:Hg19::chr16:2563989..2564006,+#_6fd4228f02b22273e846f494dd9e2039p2@ATP6V0C
8.56e-24FFCP PHASE2:Hg19::chr16:2563989..2564006,+#_6fd4228f02b22273e846f494dd9e2039p2@ATP6V0C
9.23e-24FFCP PHASE1:Hg19::chr20:35974484..35974529,+#_3092e1e582c542187477c6c03c7bc12cp2@SRC
9.23e-24FFCP PHASE2:Hg19::chr20:35974484..35974529,+#_3092e1e582c542187477c6c03c7bc12cp2@SRC
1.21e-23FFCP PHASE1:Hg19::chr12:52345448..52345532,+#_127a4f3d0e7e8ee0b5ae7884bac3c7cep1@ACVR1B
1.21e-23FFCP PHASE2:Hg19::chr12:52345448..52345532,+#_127a4f3d0e7e8ee0b5ae7884bac3c7cep1@ACVR1B
1.83e-23FFCP PHASE2:Hg19::chr7:2671611..2671658,+#_4d5506562c41be5a5e252dbc45908e17p2@TTYH3
1.83e-23FFCP PHASE1:Hg19::chr7:2671611..2671658,+#_4d5506562c41be5a5e252dbc45908e17p2@TTYH3
3.34e-23FFCP PHASE1:Hg19::chr2:110371723..110371750,-#_9b4c666c429ac4b86417fa747d312380p2@SEPT10
3.34e-23FFCP PHASE2:Hg19::chr2:110371723..110371750,-#_9b4c666c429ac4b86417fa747d312380p2@SEPT10
3.42e-23FFCP PHASE2:Hg19::chr13:77460594..77460613,-#_cb36058f760a9956782eac5d5080c2e3p3@KCTD12
3.42e-23FFCP PHASE1:Hg19::chr13:77460594..77460613,-#_cb36058f760a9956782eac5d5080c2e3p3@KCTD12
3.58e-23FFCP PHASE2:Hg19::chr9:34989685..34989748,+#_1c0f69afeeaeedb34aa76c3f81d816cfp1@DNAJB5
3.58e-23FFCP PHASE1:Hg19::chr9:34989685..34989748,+#_1c0f69afeeaeedb34aa76c3f81d816cfp1@DNAJB5
3.71e-23FFCP PHASE1:Hg19::chr17:41856305..41856363,-#_6570eb0d7125fed432119c9c1f97a9afp1@DUSP3
3.71e-23FFCP PHASE2:Hg19::chr17:41856305..41856363,-#_6570eb0d7125fed432119c9c1f97a9afp1@DUSP3
5.24e-23FFCP PHASE1:Hg19::chr11:65082349..65082378,+#_65361b8965a9845238eb7db2e7bc9df3p1@CDC42EP2
5.24e-23FFCP PHASE2:Hg19::chr11:65082349..65082378,+#_65361b8965a9845238eb7db2e7bc9df3p1@CDC42EP2
5.87e-23FFCP PHASE2:Hg19::chr6:47277634..47277651,-#_7baba93c563b08fc8553d145fd4e5ff7p1@TNFRSF21
5.87e-23FFCP PHASE1:Hg19::chr6:47277634..47277651,-#_7baba93c563b08fc8553d145fd4e5ff7p1@TNFRSF21
6.12e-23FFCP PHASE1:Hg19::chr15:64995399..64995422,-#_70968014f63ddd255cfaed37c06b7533p1@OAZ2
6.12e-23FFCP PHASE2:Hg19::chr15:64995399..64995422,-#_70968014f63ddd255cfaed37c06b7533p1@OAZ2
7.62e-23FFCP PHASE2:Hg19::chr19:44100155..44100211,-#_82d9e0c17fd7c688064a16d8a103d157p1@IRGQ
7.62e-23FFCP PHASE1:Hg19::chr19:44100155..44100211,-#_82d9e0c17fd7c688064a16d8a103d157p1@IRGQ
2.43e-22FFCP PHASE2:Hg19::chr2:127864839..127864888,-#_1f55ccdac70bfaa6369f701627afba25p2@BIN1
2.43e-22FFCP PHASE1:Hg19::chr2:127864839..127864888,-#_1f55ccdac70bfaa6369f701627afba25p2@BIN1
3.56e-22FFCP PHASE2:Hg19::chr10:125853048..125853095,-#_5bdfeded06c44f64bd3e305384451be5p2@CHST15
3.56e-22FFCP PHASE1:Hg19::chr10:125853048..125853095,-#_5bdfeded06c44f64bd3e305384451be5p2@CHST15
5.18e-22FFCP PHASE2:Hg19::chr9:14314131..14314147,-#_e9d45244b32d297eebd1df91b7c8bd49p2@NFIB
5.18e-22FFCP PHASE1:Hg19::chr9:14314131..14314147,-#_e9d45244b32d297eebd1df91b7c8bd49p2@NFIB
6.42e-22FFCP PHASE1:Hg19::chr1:249132556..249132573,+#_693f3283599ecc3e120b383ed48ea0c5p3@ZNF672
6.42e-22FFCP PHASE2:Hg19::chr1:249132556..249132573,+#_693f3283599ecc3e120b383ed48ea0c5p3@ZNF672
7.21e-22FFCP PHASE2:Hg19::chr17:73851380..73851427,-#_ed18dbfb23ab7d5e239c44219d2457e7p1@WBP2
7.21e-22FFCP PHASE1:Hg19::chr17:73851380..73851427,-#_ed18dbfb23ab7d5e239c44219d2457e7p1@WBP2
7.47e-22FFCP PHASE1:Hg19::chr3:139258443..139258485,-#_4c3b0c4379493cde02a109aa63297858p1@RBP1
7.47e-22FFCP PHASE2:Hg19::chr3:139258443..139258485,-#_4c3b0c4379493cde02a109aa63297858p1@RBP1
1.73e-21FFCP PHASE2:Hg19::chr1:23037323..23037338,+#_b0c6484fc61b8e4155972c6186c28227p1@EPHB2
1.73e-21FFCP PHASE1:Hg19::chr1:23037323..23037338,+#_b0c6484fc61b8e4155972c6186c28227p1@EPHB2
1.94e-21FFCP PHASE1:Hg19::chr22:31003154..31003188,+#_3007590311ffe814d761234cacf1f098p1@TCN2
1.94e-21FFCP PHASE2:Hg19::chr22:31003154..31003188,+#_3007590311ffe814d761234cacf1f098p1@TCN2
2.04e-21FFCP PHASE2:Hg19::chr4:24914581..24914691,-#_f89d7f656a6228eba6e9ade2f0d6f8bcp1@CCDC149
2.04e-21FFCP PHASE1:Hg19::chr4:24914581..24914691,-#_f89d7f656a6228eba6e9ade2f0d6f8bcp1@CCDC149
2.35e-21FFCP PHASE1:Hg19::chr19:6720653..6720670,-#_4b74a4363d24729fd5cdbf3dc271ae8ep1@C3
2.35e-21FFCP PHASE2:Hg19::chr19:6720653..6720670,-#_4b74a4363d24729fd5cdbf3dc271ae8ep1@C3
3.15e-21FFCP PHASE1:Hg19::chr9:14314566..14314618,-#_3ac1b634f140d5c1c77e24fb30063f1ep1@NFIB
3.15e-21FFCP PHASE2:Hg19::chr9:14314566..14314618,-#_3ac1b634f140d5c1c77e24fb30063f1ep1@NFIB
3.58e-21FFCP PHASE2:Hg19::chr5:150400145..150400158,+#_46955f758ac831e504e1c4828eb37564p1@GPX3
3.58e-21FFCP PHASE1:Hg19::chr5:150400145..150400158,+#_46955f758ac831e504e1c4828eb37564p1@GPX3
3.65e-21FFCP PHASE2:Hg19::chr4:159094160..159094185,-#_a32b73d15f1e8518b56564b7e3d51e8dp2@FAM198B
3.65e-21FFCP PHASE1:Hg19::chr4:159094160..159094185,-#_a32b73d15f1e8518b56564b7e3d51e8dp2@FAM198B
3.84e-21FFCP PHASE1:Hg19::chr10:118764649..118764683,-#_06faa221452e7a178a3195afa7774269p2@KIAA1598
3.84e-21FFCP PHASE2:Hg19::chr10:118764649..118764683,-#_06faa221452e7a178a3195afa7774269p2@KIAA1598
4.78e-21FFCP PHASE2:Hg19::chr20:4129463..4129483,+#_2f569c42b228fb89667409f405da57e7p1@SMOX
4.78e-21FFCP PHASE1:Hg19::chr20:4129463..4129483,+#_2f569c42b228fb89667409f405da57e7p1@SMOX
4.96e-21FFCP PHASE2:Hg19::chr17:7531121..7531198,-#_79d533d2f4cb9570f43589201375253ap1@SAT2
4.96e-21FFCP PHASE1:Hg19::chr17:7531121..7531198,-#_79d533d2f4cb9570f43589201375253ap1@SAT2
5.17e-21FFCP PHASE2:Hg19::chr1:10270620..10270637,+#_117cbdd681db048822443233238fd98ep1@KIF1B
5.17e-21FFCP PHASE1:Hg19::chr1:10270620..10270637,+#_117cbdd681db048822443233238fd98ep1@KIF1B
5.79e-21FFCP PHASE1:Hg19::chr1:68698197..68698214,-#_665d0b46870979a60a2007f73df29382p1@WLS
5.79e-21FFCP PHASE2:Hg19::chr1:68698197..68698214,-#_665d0b46870979a60a2007f73df29382p1@WLS
7.36e-21FFCP PHASE2:Hg19::chr3:139258521..139258589,-#_e11445fceb1ab22055b8c5431302984fp2@RBP1
7.36e-21FFCP PHASE1:Hg19::chr3:139258521..139258589,-#_e11445fceb1ab22055b8c5431302984fp2@RBP1

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