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{{UBERON
{{UBERON
|id=UBERON:0001781
|alt_id=UBERON:FMA_58617-MA_0001319-XAO_0000266
|name=layer of retina
|namespace=
|def="any of the layers that make up the retina[MP]." [MP:0003727]
|xref=AAO:0010353;;FMA:58617;;MA:0001318;;MA:0001319;;ncithesaurus:Retina_Layer;;SCTID:280657006;;XAO:0000266
|is_a=UBERON:0004121;;UBERON:0004923
|synonym="retina layer" EXACT [];;"retina neuronal layer" EXACT [MP:0006069];;"retinal layer" EXACT [];;"retinal neuronal layer" EXACT [MP:0006069]
|comment=Note that MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
|comment=Note that MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
|alt_id=UBERON:FMA_58617-MA_0001319-XAO_0000266
|disjoint_from=
|union_of=
|created_by=
|created_by=
|obo_creation_date=
|def="any of the layers that make up the retina[MP]." [MP:0003727]
|subset=vertebrate_core
|derives_from=
|derives_from=
|develops_from=
|develops_from=
|disjoint_from=
|has_quality=
|has_quality=
|id=UBERON:0001781
|is_a=UBERON:0004121 ;;UBERON:0004923
|is_obsolete=
|located_in=
|located_in=
|name=layer of retina
|namespace=FANTOM
|obo_creation_date=
|part_of=UBERON:0000966
|part_of=UBERON:0000966
|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=vertebrate_core
|preceded_by=
|synonym="retina layer" EXACT [];;"retina neuronal layer" EXACT [MP:0006069];;"retinal layer" EXACT [];;"retinal neuronal layer" EXACT [MP:0006069]
|union_of=
|xref=AAO:0010353;;FMA:58617;;MA:0001318;;MA:0001319;;ncithesaurus:Retina_Layer;;SCTID:280657006;;XAO:0000266
}}
}}

Latest revision as of 17:20, 12 September 2014

Name:layer of retina
Namespace:FANTOM
Definition:"any of the layers that make up the retina[MP]." [MP:0003727]
Xrefs:
links:

AAO:0010353
FMA:58617
MA:0001318
MA:0001319
ncithesaurus:Retina_Layer
SCTID:280657006

XAO:0000266
Synonyms: "retina layer" EXACT []
"retina neuronal layer" EXACT [MP:0006069]
"retinal layer" EXACT []
"retinal neuronal layer" EXACT [MP:0006069]
Comments:Note that MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
Alt_id: UBERON:FMA_58617-MA_0001319-XAO_0000266
Subset: 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:0004121(ectoderm-derived structure),UBERON:0004923(organ component layer)
part_of:UBERON:0000966(retina)



Children

is a:UBERON:0001782 (pigmented layer of retina),UBERON:0003902 (retinal neural layer)

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)

  • 11215-116A9 (Retinal Pigment Epithelial Cells, donor0)
  • 11528-119I7 (Retinal Pigment Epithelial Cells, donor1)
  • 11608-120I6 (Retinal Pigment Epithelial Cells, donor2)
  • 11689-122I6 (Retinal Pigment Epithelial Cells, donor3)
  • 13663-147C9 (ARPE-19 EMT induced with TGF-beta and TNF-alpha)
  • 13664-147D1 (ARPE-19 EMT induced with TGF-beta and TNF-alpha)
  • 13665-147D2 (ARPE-19 EMT induced with TGF-beta and TNF-alpha, 06hr00min, biol_rep2)
  • 13666-147D3 (ARPE-19 EMT induced with TGF-beta and TNF-alpha)
  • 13667-147D4 (ARPE-19 EMT induced with TGF-beta and TNF-alpha)
  • 13668-147D5 (ARPE-19 EMT induced with TGF-beta and TNF-alpha)

... further results


Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with UBERON:0001781 (layer of retina), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

P-valueFFCPShort description
6.94e-147FFCP PHASE2:Hg19::chr1:147150847..147150854,-#_027f8c9863ead0321c9a7c0ffc4f2b0fp@chr1:147150847..147150854, -
6.94e-147FFCP PHASE1:Hg19::chr1:147150847..147150854,-#_027f8c9863ead0321c9a7c0ffc4f2b0fp@chr1:147150847..147150854, -
8.91e-111FFCP PHASE2:Hg19::chr13:51913806..51913817,+#_d0ca610aeadd532f867636b7fd2ab5e7p2@SERPINE3
8.91e-111FFCP PHASE1:Hg19::chr13:51913806..51913817,+#_d0ca610aeadd532f867636b7fd2ab5e7p2@SERPINE3
1.3e-110FFCP PHASE1:Hg19::chr13:99135322..99135327,-#_011a71b32989c80ffeb0bc2ef8bf81dcp@chr13:99135322..99135327, -
1.3e-110FFCP PHASE2:Hg19::chr13:99135322..99135327,-#_011a71b32989c80ffeb0bc2ef8bf81dcp@chr13:99135322..99135327, -
1.55e-98FFCP PHASE1:Hg19::chr13:51913893..51913901,+#_fdc9424e075f1f358d9aa63085a04c66p@chr13:51913893..51913901, +
1.55e-98FFCP PHASE2:Hg19::chr13:51913893..51913901,+#_fdc9424e075f1f358d9aa63085a04c66p@chr13:51913893..51913901, +
2.27e-98FFCP PHASE2:Hg19::chr3:69928404..69928418,+#_ced415564f86d739d4a8c0b12226423cp@chr3:69928404..69928418, +
2.27e-98FFCP PHASE1:Hg19::chr3:69928404..69928418,+#_ced415564f86d739d4a8c0b12226423cp@chr3:69928404..69928418, +
5.72e-89FFCP PHASE1:Hg19::chr11:109990513..109990520,-#_db51547460bdf53229d5f60eaf7a3ad2p@chr11:109990513..109990520, -
5.72e-89FFCP PHASE2:Hg19::chr11:109990513..109990520,-#_db51547460bdf53229d5f60eaf7a3ad2p@chr11:109990513..109990520, -
1.41e-88FFCP PHASE2:Hg19::chr5:70308745..70308754,-#_e628563dc698ccee0992662f7ed6a05fp@chr5:70308745..70308754, -
1.41e-88FFCP PHASE1:Hg19::chr5:70308745..70308754,-#_e628563dc698ccee0992662f7ed6a05fp@chr5:70308745..70308754, -
2.01e-74FFCP PHASE2:Hg19::chr11:61522844..61522875,+#_90bacd197165f1d10103f31c41b6cdbfp2@C11orf9
2.01e-74FFCP PHASE1:Hg19::chr11:61522844..61522875,+#_90bacd197165f1d10103f31c41b6cdbfp2@C11orf9
4.26e-74FFCP PHASE2:Hg19::chr2:235591306..235591328,+#_785d897d7daec35fc5df39fb4c011180p@chr2:235591306..235591328, +
4.26e-74FFCP PHASE1:Hg19::chr2:235591306..235591328,+#_785d897d7daec35fc5df39fb4c011180p@chr2:235591306..235591328, +
5.48e-74FFCP PHASE1:Hg19::chr17:932340..932343,-#_d0649ec4cb3de2b2f429304fa2e5972ap@chr17:932340..932343, -
5.48e-74FFCP PHASE2:Hg19::chr17:932340..932343,-#_d0649ec4cb3de2b2f429304fa2e5972ap@chr17:932340..932343, -
2.4e-66FFCP PHASE1:Hg19::chr11:61522820..61522823,+#_4b8928724c3c30af7dfa955b1c3005f2p9@C11orf9
2.4e-66FFCP PHASE2:Hg19::chr11:61522820..61522823,+#_4b8928724c3c30af7dfa955b1c3005f2p9@C11orf9
3.35e-66FFCP PHASE2:Hg19::chr8:75898210..75898219,+#_2c8725d397682891a37e3f904bd03ee7p11@CRISPLD1
3.35e-66FFCP PHASE1:Hg19::chr8:75898210..75898219,+#_2c8725d397682891a37e3f904bd03ee7p11@CRISPLD1
4.67e-66FFCP PHASE2:Hg19::chr2:45166274..45166281,-#_111265eca8d2c000cc352af405041730p5@ENST00000437916
4.67e-66FFCP PHASE1:Hg19::chr2:45166274..45166281,-#_111265eca8d2c000cc352af405041730p5@ENST00000437916
2.61e-64FFCP PHASE1:Hg19::chr13:51913819..51913838,+#_2f4dd73c5f4df8a0240a9426db290750p1@SERPINE3
2.61e-64FFCP PHASE2:Hg19::chr13:51913819..51913838,+#_2f4dd73c5f4df8a0240a9426db290750p1@SERPINE3
1.18e-63FFCP PHASE2:Hg19::chr2:219610798..219610810,+#_29302811be20bca35dfb1b5486defc82p17@TTLL4
1.18e-63FFCP PHASE1:Hg19::chr2:219610798..219610810,+#_29302811be20bca35dfb1b5486defc82p17@TTLL4
1.22e-57FFCP PHASE2:Hg19::chr9:140088882..140088898,-#_48b188a4b3c511090422a850886a1e53p@chr9:140088882..140088898, -
1.22e-57FFCP PHASE1:Hg19::chr9:140088882..140088898,-#_48b188a4b3c511090422a850886a1e53p@chr9:140088882..140088898, -
2.6e-56FFCP PHASE2:Hg19::chr3:69928426..69928436,+#_93c529e237ad981d5bc56c6fc49575b6p@chr3:69928426..69928436, +
2.6e-56FFCP PHASE1:Hg19::chr3:69928426..69928436,+#_93c529e237ad981d5bc56c6fc49575b6p@chr3:69928426..69928436, +
4.58e-56FFCP PHASE1:Hg19::chr22:37633537..37633546,-#_37eee3f3e8fa0ab8e501de8d13ca7a23p@chr22:37633537..37633546, -
4.58e-56FFCP PHASE2:Hg19::chr6:168250971..168250985,+#_37eee3f3e8fa0ab8e501de8d13ca7a23p@chr6:168250971..168250985, +
4.58e-56FFCP PHASE1:Hg19::chr6:168250971..168250985,+#_37eee3f3e8fa0ab8e501de8d13ca7a23p@chr6:168250971..168250985, +
4.58e-56FFCP PHASE2:Hg19::chr22:37633537..37633546,-#_37eee3f3e8fa0ab8e501de8d13ca7a23p@chr22:37633537..37633546, -
6.68e-56FFCP PHASE1:Hg19::chr1:43533230..43533270,+#_b9118deb2eac8fc14ade4f43ea36dbcfp@chr1:43533230..43533270, +
6.68e-56FFCP PHASE2:Hg19::chr1:43533230..43533270,+#_b9118deb2eac8fc14ade4f43ea36dbcfp@chr1:43533230..43533270, +
2.37e-53FFCP PHASE2:Hg19::chr8:144905532..144905541,-#_5ea096d743f1ad841534dc2794b3feb9p6@PUF60
2.37e-53FFCP PHASE1:Hg19::chr8:144905532..144905541,-#_5ea096d743f1ad841534dc2794b3feb9p6@PUF60
3.1e-50FFCP PHASE1:Hg19::chr12:57628762..57628773,-#_2491d95be1bf4e37411c782954cfb295p@chr12:57628762..57628773, -
3.1e-50FFCP PHASE2:Hg19::chr12:57628762..57628773,-#_2491d95be1bf4e37411c782954cfb295p@chr12:57628762..57628773, -
3.1e-50FFCP PHASE1:Hg19::chr13:51913997..51914020,+#_2491d95be1bf4e37411c782954cfb295p@chr13:51913997..51914020, +
3.1e-50FFCP PHASE2:Hg19::chr13:51913997..51914020,+#_2491d95be1bf4e37411c782954cfb295p@chr13:51913997..51914020, +
3.69e-50FFCP PHASE2:Hg19::chr21:36041275..36041282,+#_2b26fc7d3d2a9331a6e3987ab5b0aeacp5@CLIC6
3.69e-50FFCP PHASE1:Hg19::chr21:36041275..36041282,+#_2b26fc7d3d2a9331a6e3987ab5b0aeacp5@CLIC6
8.47e-50FFCP PHASE2:Hg19::chr6:168251000..168251007,+#_382f4db003c933664113fe72439b0ad8p@chr6:168251000..168251007, +
8.47e-50FFCP PHASE1:Hg19::chr6:168251000..168251007,+#_382f4db003c933664113fe72439b0ad8p@chr6:168251000..168251007, +
1.97e-45FFCP PHASE2:Hg19::chr13:99135278..99135298,-#_60157593ef692beee7b00be9fa23315fp@chr13:99135278..99135298, -
1.97e-45FFCP PHASE1:Hg19::chr13:99135278..99135298,-#_60157593ef692beee7b00be9fa23315fp@chr13:99135278..99135298, -
1.67e-41FFCP PHASE2:Hg19::chr3:69928371..69928385,+#_ff9a80b1ad8bddae36b648da32a93eddp@chr3:69928371..69928385, +
1.67e-41FFCP PHASE1:Hg19::chr3:69928371..69928385,+#_ff9a80b1ad8bddae36b648da32a93eddp@chr3:69928371..69928385, +
2.2e-41FFCP PHASE1:Hg19::chr14:87636652..87636657,-#_a8a22e4469f9b6426d16fdf27ae7c941p@chr14:87636652..87636657, -
2.2e-41FFCP PHASE2:Hg19::chr14:87636652..87636657,-#_a8a22e4469f9b6426d16fdf27ae7c941p@chr14:87636652..87636657, -
7.56e-41FFCP PHASE2:Hg19::chr12:78359999..78360035,+#_e9623f5136dba86698c3b038f7d6f67cp13@NAV3
7.56e-41FFCP PHASE1:Hg19::chr12:78359999..78360035,+#_e9623f5136dba86698c3b038f7d6f67cp13@NAV3
1.81e-40FFCP PHASE2:Hg19::chr2:235591286..235591298,+#_6f394c7b7fc120696285ed08d1c75991p@chr2:235591286..235591298, +
1.81e-40FFCP PHASE1:Hg19::chr2:235591286..235591298,+#_6f394c7b7fc120696285ed08d1c75991p@chr2:235591286..235591298, +
4.94e-40FFCP PHASE1:Hg19::chr11:119217442..119217445,-#_7dfbf0f564214c5667fe82c50fa31e7ep5@MFRP, p6@C1QTNF5
4.94e-40FFCP PHASE2:Hg19::chr11:119217442..119217445,-#_7dfbf0f564214c5667fe82c50fa31e7ep5@MFRP, p6@C1QTNF5
4.94e-40FFCP PHASE2:Hg19::chr16:84228961..84228982,+#_7dfbf0f564214c5667fe82c50fa31e7ep@chr16:84228961..84228982, +
4.94e-40FFCP PHASE1:Hg19::chr16:84228961..84228982,+#_7dfbf0f564214c5667fe82c50fa31e7ep@chr16:84228961..84228982, +
1.75e-38FFCP PHASE2:Hg19::chr3:45837959..45837973,-#_2afb3bdf84b8ffb9a6daf0f2a33bf877p3@SLC6A20
1.75e-38FFCP PHASE1:Hg19::chr3:45837959..45837973,-#_2afb3bdf84b8ffb9a6daf0f2a33bf877p3@SLC6A20
2.78e-38FFCP PHASE2:Hg19::chr21:36041264..36041274,+#_c8377577e61f068f541ae6f0da731564p3@CLIC6
2.78e-38FFCP PHASE1:Hg19::chr21:36041264..36041274,+#_c8377577e61f068f541ae6f0da731564p3@CLIC6
4.61e-38FFCP PHASE1:Hg19::chr11:75201755..75201762,-#_c13b8f3b5abd21993b117ce2e11ece28p7@GDPD5
4.61e-38FFCP PHASE2:Hg19::chr11:75201755..75201762,-#_c13b8f3b5abd21993b117ce2e11ece28p7@GDPD5
1.26e-37FFCP PHASE1:Hg19::chr11:119217421..119217435,-#_058013fc2b5d294f1502fa7705ef602dp4@MFRP, p5@C1QTNF5
1.26e-37FFCP PHASE2:Hg19::chr11:119217421..119217435,-#_058013fc2b5d294f1502fa7705ef602dp4@MFRP, p5@C1QTNF5
5.06e-34FFCP PHASE1:Hg19::chr17:932596..932605,-#_120ab7ba3631099f290aacd96cc94262p@chr17:932596..932605, -
5.06e-34FFCP PHASE2:Hg19::chr8:22411813..22411825,+#_120ab7ba3631099f290aacd96cc94262p55@SORBS3
5.06e-34FFCP PHASE1:Hg19::chr8:22411813..22411825,+#_120ab7ba3631099f290aacd96cc94262p55@SORBS3
5.06e-34FFCP PHASE2:Hg19::chr17:932596..932605,-#_120ab7ba3631099f290aacd96cc94262p@chr17:932596..932605, -
8.36e-34FFCP PHASE2:Hg19::chr22:38480132..38480159,-#_c51c894a69b6baf45f94f943c0d78115p1@SLC16A8
8.36e-34FFCP PHASE1:Hg19::chr22:38480132..38480159,-#_c51c894a69b6baf45f94f943c0d78115p1@SLC16A8
8.36e-34FFCP PHASE2:Hg19::chr20:52790691..52790695,-#_c51c894a69b6baf45f94f943c0d78115p5@CYP24A1
8.36e-34FFCP PHASE1:Hg19::chr20:52790691..52790695,-#_c51c894a69b6baf45f94f943c0d78115p5@CYP24A1
1.38e-33FFCP PHASE2:Hg19::chr3:98672197..98672201,+#_6c8938b22984a1f6574a80e433215868p@chr3:98672197..98672201, +
1.38e-33FFCP PHASE1:Hg19::chr3:98672197..98672201,+#_6c8938b22984a1f6574a80e433215868p@chr3:98672197..98672201, +
1.63e-33FFCP PHASE2:Hg19::chr3:183733654..183733680,-#_509636d1bab482fe419be5d02d2fed61p@chr3:183733654..183733680, -
1.63e-33FFCP PHASE1:Hg19::chr3:183733654..183733680,-#_509636d1bab482fe419be5d02d2fed61p@chr3:183733654..183733680, -
1.63e-33FFCP PHASE2:Hg19::chr9:127025189..127025200,+#_509636d1bab482fe419be5d02d2fed61p1@ENST00000437461
1.63e-33FFCP PHASE1:Hg19::chr9:127025189..127025200,+#_509636d1bab482fe419be5d02d2fed61p1@ENST00000437461
6.19e-33FFCP PHASE1:Hg19::chr14:28081776..28081788,+#_5dd297473a8342411968c67a7a0e95a0p1@LOC100505967
6.19e-33FFCP PHASE2:Hg19::chr14:28081776..28081788,+#_5dd297473a8342411968c67a7a0e95a0p1@LOC100505967
1.18e-32FFCP PHASE2:Hg19::chr2:45169172..45169177,+#_dfa8f437d0642bb2cd05b25fe2999d4ep11@SIX3
1.18e-32FFCP PHASE1:Hg19::chr2:45169172..45169177,+#_dfa8f437d0642bb2cd05b25fe2999d4ep11@SIX3
1.64e-32FFCP PHASE2:Hg19::chr5:33984786..33984820,-#_7a280d00016f0c933d4c53b006172660p2@SLC45A2
1.64e-32FFCP PHASE1:Hg19::chr5:33984786..33984820,-#_7a280d00016f0c933d4c53b006172660p2@SLC45A2
5.16e-32FFCP PHASE2:Hg19::chr15:31393917..31393936,-#_5dbc4ce8dde71e126c68aa824ea09cc8p1@TRPM1
5.16e-32FFCP PHASE1:Hg19::chr15:31393917..31393936,-#_5dbc4ce8dde71e126c68aa824ea09cc8p1@TRPM1
4.66e-31FFCP PHASE2:Hg19::chr16:68301840..68301845,+#_b5257190b84af9c9dc8474fd52b0e329p@chr16:68301840..68301845, +
4.66e-31FFCP PHASE1:Hg19::chr16:68301840..68301845,+#_b5257190b84af9c9dc8474fd52b0e329p@chr16:68301840..68301845, +
9.47e-31FFCP PHASE2:Hg19::chr19:49140255..49140268,-#_44db50fcd402555df52d7a18136809e9p9@DBP
9.47e-31FFCP PHASE1:Hg19::chr19:49140255..49140268,-#_44db50fcd402555df52d7a18136809e9p9@DBP
1.16e-30FFCP PHASE2:Hg19::chr12:52579447..52579461,-#_c3cdef0059c0c96f3cc74e3b6c9459acp6@KRT80
1.16e-30FFCP PHASE1:Hg19::chr12:52579447..52579461,-#_c3cdef0059c0c96f3cc74e3b6c9459acp6@KRT80

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