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{{UBERON
{{UBERON
|id=UBERON:0000923
|name=germ layer
|namespace=
|def="A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm." [Wikipedia:Germ_layer]
|xref=AAO:0000480;;BILA:0000035;;BTO:0000556;;FBbt:00000110;;FMA:69069;;GAID:1303;;MESH:A.16.254.425;;ncithesaurus:Embryonic_Tissue;;ncithesaurus:Germinal_Layer;;TAO:0001122;;VHOG:0001223;;XAO:0003011;;ZFA:0001122
|is_a=UBERON:0000479;;UBERON:0005291
|synonym="embryonic germ layer" RELATED [];;"embryonic germ layers" RELATED [];;"embryonic tissue" BROAD [FMA:69069];;"germinal layer" EXACT [ncithesaurus:Germinal_Layer];;"primary germ layer" EXACT [GO:0001704, ZFA:0001122]
|comment=
|alt_id=UBERON:FBbt_00000110-FMA_69069;;UBERON:XAO_0003011-ZFA_0001122
|alt_id=UBERON:FBbt_00000110-FMA_69069;;UBERON:XAO_0003011-ZFA_0001122
|disjoint_from=
|comment=Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary
|union_of=
|created_by=
|created_by=
|obo_creation_date=
|def="A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm." [Wikipedia:Germ_layer]
|subset=uberon_slim;;vertebrate_core
|adjacent_to=
|derives_from=
|derives_from=
|develops_from=UBERON:0002532
|develops_from=UBERON:0002532
|disjoint_from=
|has_quality=
|has_quality=
|id=UBERON:0000923
|is_a=UBERON:0010316
|is_obsolete=
|located_in=
|located_in=
|name=germ layer
|namespace=FANTOM
|obo_creation_date=
|part_of=UBERON:0000922
|part_of=UBERON:0000922
|preceded_by=
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|is_obsolete=
|subset=uberon_slim;;vertebrate_core
|preceded_by=
|synonym="embryonic germ layer" RELATED [];;"embryonic germ layers" RELATED [];;"embryonic tissue" BROAD [FMA:69069];;"germinal layer" EXACT [ncithesaurus:Germinal_Layer];;"primary germ layer" NARROW [GO:0001704, ZFA:0001122]
|union_of=
|xref=AAO:0000480;;BILA:0000035;;BTO:0000556;;FBbt:00000110;;FMA:69069;;GAID:1303;;MESH:A.16.254.425;;ncithesaurus:Embryonic_Tissue;;ncithesaurus:Germinal_Layer;;TAO:0001122;;VHOG:0001223;;XAO:0003011;;ZFA:0001122
}}
}}

Latest revision as of 17:11, 12 September 2014

Name:germ layer
Namespace:FANTOM
Definition:"A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm." [Wikipedia:Germ_layer]
Xrefs:
links:

AAO:0000480
BILA:0000035
BTO:0000556
FBbt:00000110
FMA:69069
GAID:1303
MESH:A.16.254.425
ncithesaurus:Embryonic_Tissue
ncithesaurus:Germinal_Layer
TAO:0001122
VHOG:0001223
XAO:0003011

ZFA:0001122
Synonyms: "embryonic germ layer" RELATED []
"embryonic germ layers" RELATED []
"embryonic tissue" BROAD [FMA:69069]
"germinal layer" EXACT [ncithesaurus:Germinal_Layer]
"primary germ layer" NARROW [GO:0001704, ZFA:0001122]
Comments:Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary
Alt_id: UBERON:FBbt_00000110-FMA_69069
UBERON:XAO_0003011-ZFA_0001122
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:0010316(germ layer / neural crest)
develops_from:UBERON:0002532(epiblast (generic))
part_of:UBERON:0000922(embryo)



Children

is a:UBERON:0000924 (ectoderm),UBERON:0000925 (endoderm),UBERON:0000926 (mesoderm),UBERON:0002346 (neurectoderm)

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)

Mouse (Mus musculus)


Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with UBERON:0000923 (germ layer), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

P-valueFFCPShort description
7.5e-31FFCP PHASE1:Hg19::chr20:23618584..23618603,-#_d6fc19a7935890aa127aa8226f2a77b1p1@CST3
7.5e-31FFCP PHASE2:Hg19::chr20:23618584..23618603,-#_d6fc19a7935890aa127aa8226f2a77b1p1@CST3
6.91e-29FFCP PHASE1:Hg19::chr13:77460532..77460548,-#_a9ebc310222e830145786a1c53f94285p1@KCTD12
6.91e-29FFCP PHASE2:Hg19::chr13:77460532..77460548,-#_a9ebc310222e830145786a1c53f94285p1@KCTD12
1.31e-28FFCP PHASE1:Hg19::chr13:45010939..45011033,-#_d8d653de90b864f52d9351b3f9c2af1dp1@TSC22D1
1.31e-28FFCP PHASE2:Hg19::chr13:45010939..45011033,-#_d8d653de90b864f52d9351b3f9c2af1dp1@TSC22D1
6.82e-28FFCP PHASE1:Hg19::chr2:230135937..230136016,-#_e6ffb7204cafbc0d6a26a432cd3ca7f6p1@PID1
6.82e-28FFCP PHASE2:Hg19::chr2:230135937..230136016,-#_e6ffb7204cafbc0d6a26a432cd3ca7f6p1@PID1
1.74e-26FFCP PHASE1:Hg19::chr7:111846435..111846471,-#_a1955bf30b0a6ebc77e5d9ecdab72a40p1@DOCK4
1.74e-26FFCP PHASE2:Hg19::chr7:111846435..111846471,-#_a1955bf30b0a6ebc77e5d9ecdab72a40p1@DOCK4
4.12e-26FFCP PHASE2:Hg19::chr11:1330834..1330875,-#_ebb0d9346463e698d10761cfc8125479p1@TOLLIP
4.12e-26FFCP PHASE1:Hg19::chr11:1330834..1330875,-#_ebb0d9346463e698d10761cfc8125479p1@TOLLIP
6.68e-25FFCP PHASE1:Hg19::chr12:112204714..112204781,+#_e283cbc56498575bfafff9d7a0e78ff8p1@ALDH2
6.68e-25FFCP PHASE2:Hg19::chr12:112204714..112204781,+#_e283cbc56498575bfafff9d7a0e78ff8p1@ALDH2
6.83e-25FFCP PHASE2:Hg19::chr13:77460594..77460613,-#_3f7cd83d0e6cb39f7bfb2d4459584baap3@KCTD12
6.83e-25FFCP PHASE1:Hg19::chr13:77460594..77460613,-#_3f7cd83d0e6cb39f7bfb2d4459584baap3@KCTD12
1.27e-24FFCP PHASE2:Hg19::chr4:85887789..85887862,-#_bd4de7d31d7b762dabddc72b76c5fadcp1@WDFY3
1.27e-24FFCP PHASE1:Hg19::chr4:85887789..85887862,-#_bd4de7d31d7b762dabddc72b76c5fadcp1@WDFY3
6.07e-24FFCP PHASE2:Hg19::chr16:4852616..4852679,-#_04c126eafca524c0df0f522b2a4d97fcp1@ROGDI
6.07e-24FFCP PHASE1:Hg19::chr16:4852616..4852679,-#_04c126eafca524c0df0f522b2a4d97fcp1@ROGDI
1.62e-23FFCP PHASE1:Hg19::chr1:183774240..183774270,+#_2aab48f21caba8399f7ef1f6e8282ef3p1@RGL1
1.62e-23FFCP PHASE2:Hg19::chr1:183774240..183774270,+#_2aab48f21caba8399f7ef1f6e8282ef3p1@RGL1
2.33e-23FFCP PHASE1:Hg19::chr8:30670289..30670354,-#_81d39089bd998172657a1e0c6d9403fdp1@PPP2CB
2.33e-23FFCP PHASE2:Hg19::chr8:30670289..30670354,-#_81d39089bd998172657a1e0c6d9403fdp1@PPP2CB
2.57e-23FFCP PHASE1:Hg19::chr13:77460635..77460654,-#_908f379a9abcc36010bb74ff9d98acc7p2@KCTD12
2.57e-23FFCP PHASE2:Hg19::chr13:77460635..77460654,-#_908f379a9abcc36010bb74ff9d98acc7p2@KCTD12
4.06e-23FFCP PHASE1:Hg19::chr4:159094160..159094185,-#_88a913c4cd8ac89a6837a75014fdd8abp2@FAM198B
4.06e-23FFCP PHASE2:Hg19::chr4:159094160..159094185,-#_88a913c4cd8ac89a6837a75014fdd8abp2@FAM198B
6.15e-23FFCP PHASE1:Hg19::chr15:90456156..90456198,-#_bda1b97e988205eb09e8ccea398e6fc8p1@C15orf38
6.15e-23FFCP PHASE2:Hg19::chr15:90456156..90456198,-#_bda1b97e988205eb09e8ccea398e6fc8p1@C15orf38
7.82e-23FFCP PHASE2:Hg19::chr19:40871734..40871809,+#_879021b9cbe0c087dae3166a65155a81p1@PLD3
7.82e-23FFCP PHASE1:Hg19::chr19:40871734..40871809,+#_879021b9cbe0c087dae3166a65155a81p1@PLD3
1.53e-22FFCP PHASE2:Hg19::chr16:2563989..2564006,+#_77a6f41d8665242d0bf5c33d022607b9p2@ATP6V0C
1.53e-22FFCP PHASE1:Hg19::chr16:2563989..2564006,+#_77a6f41d8665242d0bf5c33d022607b9p2@ATP6V0C
2.37e-22FFCP PHASE1:Hg19::chr20:35974484..35974529,+#_8ae59601ad95cc68d3c66e56709cbc6ap2@SRC
2.37e-22FFCP PHASE2:Hg19::chr20:35974484..35974529,+#_8ae59601ad95cc68d3c66e56709cbc6ap2@SRC
5.65e-22FFCP PHASE2:Hg19::chr11:65082349..65082378,+#_3eac2ff2c5b47a61ffee050e917983b5p1@CDC42EP2
5.65e-22FFCP PHASE1:Hg19::chr11:65082349..65082378,+#_3eac2ff2c5b47a61ffee050e917983b5p1@CDC42EP2
5.66e-22FFCP PHASE2:Hg19::chr17:1466030..1466129,-#_9433b375a565b8a947cd7fc21bd3630fp1@PITPNA
5.66e-22FFCP PHASE1:Hg19::chr17:1466030..1466129,-#_9433b375a565b8a947cd7fc21bd3630fp1@PITPNA
5.93e-22FFCP PHASE1:Hg19::chr19:6720653..6720670,-#_9ad84dd29bbde729eac0230f1333b07fp1@C3
5.93e-22FFCP PHASE2:Hg19::chr19:6720653..6720670,-#_9ad84dd29bbde729eac0230f1333b07fp1@C3
6.18e-22FFCP PHASE2:Hg19::chr7:2671611..2671658,+#_7292137bb57bc45a6efea5c433f93f08p2@TTYH3
6.18e-22FFCP PHASE1:Hg19::chr7:2671611..2671658,+#_7292137bb57bc45a6efea5c433f93f08p2@TTYH3
1.1e-21FFCP PHASE1:Hg19::chr2:127864839..127864888,-#_5104a88350d2ec3a7ad8638b0faf84abp2@BIN1
1.1e-21FFCP PHASE2:Hg19::chr2:127864839..127864888,-#_5104a88350d2ec3a7ad8638b0faf84abp2@BIN1
2.41e-21FFCP PHASE2:Hg19::chr17:73851380..73851427,-#_4ec43c68e7c8ec63509d62ac512c6b7ep1@WBP2
2.41e-21FFCP PHASE1:Hg19::chr17:73851380..73851427,-#_4ec43c68e7c8ec63509d62ac512c6b7ep1@WBP2
3.59e-21FFCP PHASE1:Hg19::chr22:31003154..31003188,+#_37f263711065b8140c1c346f21d88471p1@TCN2
3.59e-21FFCP PHASE2:Hg19::chr22:31003154..31003188,+#_37f263711065b8140c1c346f21d88471p1@TCN2
3.69e-21FFCP PHASE1:Hg19::chr9:14314566..14314618,-#_0cbe13bcc973d943af8b833eec481fd2p1@NFIB
3.69e-21FFCP PHASE2:Hg19::chr9:14314566..14314618,-#_0cbe13bcc973d943af8b833eec481fd2p1@NFIB
4.02e-21FFCP PHASE1:Hg19::chr9:14314131..14314147,-#_78a901a6d350e6ff0ffcdf550a5b35cep2@NFIB
4.02e-21FFCP PHASE2:Hg19::chr9:14314131..14314147,-#_78a901a6d350e6ff0ffcdf550a5b35cep2@NFIB
4.54e-21FFCP PHASE1:Hg19::chr19:44100155..44100211,-#_0d82654cd3e27d6ddffb2208f68f6ea4p1@IRGQ
4.54e-21FFCP PHASE2:Hg19::chr19:44100155..44100211,-#_0d82654cd3e27d6ddffb2208f68f6ea4p1@IRGQ
5.7e-21FFCP PHASE2:Hg19::chr4:24914581..24914691,-#_9747b694071a2a740c8d3f5732aaee0ep1@CCDC149
5.7e-21FFCP PHASE1:Hg19::chr4:24914581..24914691,-#_9747b694071a2a740c8d3f5732aaee0ep1@CCDC149
6.27e-21FFCP PHASE1:Hg19::chr2:127864608..127864688,-#_c9272e8d859e8d60ed1fd5ff1dbc401fp1@BIN1
6.27e-21FFCP PHASE2:Hg19::chr2:127864608..127864688,-#_c9272e8d859e8d60ed1fd5ff1dbc401fp1@BIN1
1.02e-20FFCP PHASE1:Hg19::chr19:14228541..14228582,-#_29cbdb6ff17f8c11fcfa5474c49daba4p1@PRKACA
1.02e-20FFCP PHASE2:Hg19::chr19:14228541..14228582,-#_29cbdb6ff17f8c11fcfa5474c49daba4p1@PRKACA
1.29e-20FFCP PHASE2:Hg19::chr16:89787269..89787359,-#_32a44ca7ff296e85dbb977626201e6b8p1@C16orf7
1.29e-20FFCP PHASE1:Hg19::chr16:89787269..89787359,-#_32a44ca7ff296e85dbb977626201e6b8p1@C16orf7
1.45e-20FFCP PHASE1:Hg19::chr1:10270620..10270637,+#_d3cab075e34a1b348d370a8781187ba7p1@KIF1B
1.45e-20FFCP PHASE2:Hg19::chr1:10270620..10270637,+#_d3cab075e34a1b348d370a8781187ba7p1@KIF1B
2.63e-20FFCP PHASE2:Hg19::chr18:59561635..59561651,-#_3c1b83d380a086de20aeae4da87bb46ep@chr18:59561635..59561651, -
2.63e-20FFCP PHASE1:Hg19::chr18:59561635..59561651,-#_3c1b83d380a086de20aeae4da87bb46ep@chr18:59561635..59561651, -
3.08e-20FFCP PHASE1:Hg19::chr12:52345448..52345532,+#_9cd7d920dc88a2f104e087ac6fa05758p1@ACVR1B
3.08e-20FFCP PHASE2:Hg19::chr12:52345448..52345532,+#_9cd7d920dc88a2f104e087ac6fa05758p1@ACVR1B
3.96e-20FFCP PHASE1:Hg19::chr20:23614485..23614564,-#_d945d05c7665df876afa9b2693f58890p@chr20:23614485..23614564, -
3.96e-20FFCP PHASE2:Hg19::chr20:23614485..23614564,-#_d945d05c7665df876afa9b2693f58890p@chr20:23614485..23614564, -
5.35e-20FFCP PHASE1:Hg19::chr1:68698197..68698214,-#_4ae723b24b216d1d0b51519df4e53a65p1@WLS
5.35e-20FFCP PHASE2:Hg19::chr1:68698197..68698214,-#_4ae723b24b216d1d0b51519df4e53a65p1@WLS
6.51e-20FFCP PHASE1:Hg19::chr10:30025922..30025958,-#_5bc82df75fae44bbbe6fa901620014fbp3@SVIL
6.51e-20FFCP PHASE2:Hg19::chr10:30025922..30025958,-#_5bc82df75fae44bbbe6fa901620014fbp3@SVIL
6.99e-20FFCP PHASE1:Hg19::chr15:64995399..64995422,-#_6addeff24c7edbadb54ffc2089d92f52p1@OAZ2
6.99e-20FFCP PHASE2:Hg19::chr15:64995399..64995422,-#_6addeff24c7edbadb54ffc2089d92f52p1@OAZ2
8.06e-20FFCP PHASE1:Hg19::chr9:34989685..34989748,+#_7505cc211ab864f8714b4a3533168941p1@DNAJB5
8.06e-20FFCP PHASE2:Hg19::chr9:34989685..34989748,+#_7505cc211ab864f8714b4a3533168941p1@DNAJB5
9.9e-20FFCP PHASE1:Hg19::chrX:100333858..100333876,+#_43d225730c8ebfb91eb54c9993e317f9p1@TMEM35
9.9e-20FFCP PHASE2:Hg19::chrX:100333858..100333876,+#_43d225730c8ebfb91eb54c9993e317f9p1@TMEM35
1.09e-19FFCP PHASE1:Hg19::chr16:2563941..2563983,+#_fdda434a236b1d2c234bf528bbbf7c0cp1@ATP6V0C
1.09e-19FFCP PHASE2:Hg19::chr16:2563941..2563983,+#_fdda434a236b1d2c234bf528bbbf7c0cp1@ATP6V0C
1.11e-19FFCP PHASE1:Hg19::chr17:68165657..68165688,+#_cdda5b2c98f92ba10ef9599dde506823p1@KCNJ2
1.11e-19FFCP PHASE2:Hg19::chr17:68165657..68165688,+#_cdda5b2c98f92ba10ef9599dde506823p1@KCNJ2
1.12e-19FFCP PHASE2:Hg19::chr17:7492684..7492778,-#_65e6728cabde2eb76c6197b88eba41e4p2@SOX15
1.12e-19FFCP PHASE1:Hg19::chr17:7492684..7492778,-#_65e6728cabde2eb76c6197b88eba41e4p2@SOX15
1.16e-19FFCP PHASE1:Hg19::chr19:11466086..11466159,+#_8ee9ae46731709a8c547815fd40dd235p1@LPPR2
1.16e-19FFCP PHASE2:Hg19::chr19:11466086..11466159,+#_8ee9ae46731709a8c547815fd40dd235p1@LPPR2
1.32e-19FFCP PHASE2:Hg19::chr18:59561658..59561685,-#_6e9e1dabe916c3754e8a3943f5d54cafp@chr18:59561658..59561685, -
1.32e-19FFCP PHASE1:Hg19::chr18:59561658..59561685,-#_6e9e1dabe916c3754e8a3943f5d54cafp@chr18:59561658..59561685, -
1.38e-19FFCP PHASE1:Hg19::chr12:110719036..110719113,+#_e1280981aa8926b063a2333b79dbb56ep1@ATP2A2
1.38e-19FFCP PHASE2:Hg19::chr12:110719036..110719113,+#_e1280981aa8926b063a2333b79dbb56ep1@ATP2A2
1.45e-19FFCP PHASE1:Hg19::chr6:123110389..123110441,+#_d26c4c52689e8513bc08f09264875664p1@SMPDL3A
1.45e-19FFCP PHASE2:Hg19::chr6:123110389..123110441,+#_d26c4c52689e8513bc08f09264875664p1@SMPDL3A
1.86e-19FFCP PHASE1:Hg19::chr10:118764649..118764683,-#_e76b7a83cfb20f13d8d599fc875fd563p2@KIAA1598
1.86e-19FFCP PHASE2:Hg19::chr10:118764649..118764683,-#_e76b7a83cfb20f13d8d599fc875fd563p2@KIAA1598
3.3e-19FFCP PHASE2:Hg19::chr2:153191678..153191697,+#_97ae24432c2583828d0547c10f23016bp1@FMNL2
3.3e-19FFCP PHASE1:Hg19::chr2:153191678..153191697,+#_97ae24432c2583828d0547c10f23016bp1@FMNL2

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