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UBERON:0001782

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Name:pigmented layer of retina
Namespace:FANTOM
Definition:"A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP]." [Wikipedia:Retinal_pigment_epithelium, ZFIN:curator]
Xrefs:
links:

AAO:0011096
BTO:0001177
EHDAA2:0001465
EHDAA:4765
EMAPA:17172
FMA:58627
[ Gray881.png Gray881.png]
[ 200px-Gray881.png 200px-Gray881.png]
MA:0000279
ncithesaurus:Retinal_Pigment_Epithelium
SCTID:280662007
TAO:0000144
VHOG:0000536
XAO:0003217

ZFA:0000144
Synonyms: "epithelium, retinal pigment" RELATED [BTO:0001177]
"outer pigmented layer of retina" EXACT []
"pigment epithelium of retina" EXACT []
"pigmented epithelium" RELATED []
"pigmented retina" RELATED []
"pigmented retinal epithelium" EXACT []
"PRE" RELATED []
"retinal pigment epithelium" EXACT [MP:0005201, Wikipedia:Retinal_pigment_epithelium]
"retinal pigmented epithelium" EXACT [ZFA:0000144]
"RPE" RELATED []
"stratum pigmentosa retinae, p. pigmentosa retinae" RELATED LATIN [Wikipedia:Retinal_pigment_epithelium]
"stratum pigmentosum (retina)" EXACT []
Comments:editor note - we follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers
Alt_id: UBERON:FMA_58627-MA_0000279-ZFA_0000144
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:0001781(layer of retina),UBERON:0015808(eye epithelium)
develops_from:UBERON:0005424(presumptive retinal pigmented epithelium)



Children

part of:CL:0002586 (retinal pigment epithelial cell)

Ontology Tree: Loaded from BioPortal

Ontorolgy tree(Small window open)

FF samples
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:0001782 (pigmented layer of retina), sorted by p-values
Analyst: Hideya Kawaji

link to source dataset
human : data
mouse : data

P-valueFFCPShort description
2.79e-195FFCP PHASE1:Hg19::chr1:147150847..147150854,-#_9f7dbf71f3f059a0b649bc64883f1acfp@chr1:147150847..147150854, -
2.79e-195FFCP PHASE2:Hg19::chr1:147150847..147150854,-#_9f7dbf71f3f059a0b649bc64883f1acfp@chr1:147150847..147150854, -
3.27e-147FFCP PHASE1:Hg19::chr13:51913806..51913817,+#_49fdb21af4217d755cf58630b9af4de8p2@SERPINE3
3.27e-147FFCP PHASE2:Hg19::chr13:51913806..51913817,+#_49fdb21af4217d755cf58630b9af4de8p2@SERPINE3
5.41e-147FFCP PHASE2:Hg19::chr13:99135322..99135327,-#_cfb12de3bf771a66d1f6bac56c743447p@chr13:99135322..99135327, -
5.41e-147FFCP PHASE1:Hg19::chr13:99135322..99135327,-#_cfb12de3bf771a66d1f6bac56c743447p@chr13:99135322..99135327, -
8.98e-131FFCP PHASE1:Hg19::chr13:51913893..51913901,+#_18709429f3383a3d05e54b02e1c6a4b8p@chr13:51913893..51913901, +
8.98e-131FFCP PHASE2:Hg19::chr13:51913893..51913901,+#_18709429f3383a3d05e54b02e1c6a4b8p@chr13:51913893..51913901, +
3.48e-118FFCP PHASE2:Hg19::chr11:109990513..109990520,-#_c0f14d5c475472a051b78a26ec829852p@chr11:109990513..109990520, -
3.48e-118FFCP PHASE1:Hg19::chr11:109990513..109990520,-#_c0f14d5c475472a051b78a26ec829852p@chr11:109990513..109990520, -
1.16e-117FFCP PHASE1:Hg19::chr5:70308745..70308754,-#_631d53ddc1285555b696a2d0cfd7a00bp@chr5:70308745..70308754, -
1.16e-117FFCP PHASE2:Hg19::chr5:70308745..70308754,-#_631d53ddc1285555b696a2d0cfd7a00bp@chr5:70308745..70308754, -
7.95e-99FFCP PHASE2:Hg19::chr11:61522844..61522875,+#_d2747888d77ce46c3775f0bd1488c9c9p2@C11orf9
7.95e-99FFCP PHASE1:Hg19::chr11:61522844..61522875,+#_d2747888d77ce46c3775f0bd1488c9c9p2@C11orf9
2.17e-98FFCP PHASE2:Hg19::chr2:235591306..235591328,+#_2eba63f9e0336435c31f0a531b38ac42p@chr2:235591306..235591328, +
2.17e-98FFCP PHASE1:Hg19::chr2:235591306..235591328,+#_2eba63f9e0336435c31f0a531b38ac42p@chr2:235591306..235591328, +
6.24e-88FFCP PHASE2:Hg19::chr11:61522820..61522823,+#_d145b750f5c88c6cb57128ae810aa56fp9@C11orf9
6.24e-88FFCP PHASE1:Hg19::chr11:61522820..61522823,+#_d145b750f5c88c6cb57128ae810aa56fp9@C11orf9
9.74e-88FFCP PHASE2:Hg19::chr8:75898210..75898219,+#_df552b259893dd7ba36ce8fe6b1f3070p11@CRISPLD1
9.74e-88FFCP PHASE1:Hg19::chr8:75898210..75898219,+#_df552b259893dd7ba36ce8fe6b1f3070p11@CRISPLD1
1.52e-87FFCP PHASE2:Hg19::chr2:45166274..45166281,-#_dc4ba13c7b3a08b99b70a00e330b2456p5@ENST00000437916
1.52e-87FFCP PHASE1:Hg19::chr2:45166274..45166281,-#_dc4ba13c7b3a08b99b70a00e330b2456p5@ENST00000437916
2.28e-85FFCP PHASE1:Hg19::chr13:51913819..51913838,+#_82143b06b3bec80f0dbf904fbc4963d4p1@SERPINE3
2.28e-85FFCP PHASE2:Hg19::chr13:51913819..51913838,+#_82143b06b3bec80f0dbf904fbc4963d4p1@SERPINE3
1.01e-74FFCP PHASE1:Hg19::chr3:69928426..69928436,+#_c5768543d2edab0842d00f1a4fe663b2p@chr3:69928426..69928436, +
1.01e-74FFCP PHASE2:Hg19::chr3:69928426..69928436,+#_c5768543d2edab0842d00f1a4fe663b2p@chr3:69928426..69928436, +
1.29e-74FFCP PHASE1:Hg19::chr3:69928404..69928418,+#_90461782acdc02205385827845cd0df0p@chr3:69928404..69928418, +
1.29e-74FFCP PHASE2:Hg19::chr3:69928404..69928418,+#_90461782acdc02205385827845cd0df0p@chr3:69928404..69928418, +
2.14e-74FFCP PHASE1:Hg19::chr22:37633537..37633546,-#_1cb67501a155134dc7b0a32941ccdd62p@chr22:37633537..37633546, -
2.14e-74FFCP PHASE2:Hg19::chr6:168250971..168250985,+#_1cb67501a155134dc7b0a32941ccdd62p@chr6:168250971..168250985, +
2.14e-74FFCP PHASE1:Hg19::chr6:168250971..168250985,+#_1cb67501a155134dc7b0a32941ccdd62p@chr6:168250971..168250985, +
2.14e-74FFCP PHASE2:Hg19::chr22:37633537..37633546,-#_1cb67501a155134dc7b0a32941ccdd62p@chr22:37633537..37633546, -
3.54e-74FFCP PHASE1:Hg19::chr1:43533230..43533270,+#_2e92c2118ab60fa49ffbc03677e8bfcfp@chr1:43533230..43533270, +
3.54e-74FFCP PHASE2:Hg19::chr1:43533230..43533270,+#_2e92c2118ab60fa49ffbc03677e8bfcf+, p@chr1:43533230..43533270
1.54e-66FFCP PHASE2:Hg19::chr21:36041275..36041282,+#_d74bba9507044d4ca1674286d61af093p5@CLIC6
1.54e-66FFCP PHASE1:Hg19::chr21:36041275..36041282,+#_d74bba9507044d4ca1674286d61af093p5@CLIC6
2.39e-66FFCP PHASE1:Hg19::chr13:51913997..51914020,+#_dd9cad35948d1ec74da6d3acb6936b24p@chr13:51913997..51914020, +
2.39e-66FFCP PHASE2:Hg19::chr13:51913997..51914020,+#_dd9cad35948d1ec74da6d3acb6936b24p@chr13:51913997..51914020, +
6.53e-66FFCP PHASE1:Hg19::chr6:168251000..168251007,+#_9e31e9b81a6bd80ebdb5a4b0e6b87493p@chr6:168251000..168251007, +
6.53e-66FFCP PHASE2:Hg19::chr6:168251000..168251007,+#_9e31e9b81a6bd80ebdb5a4b0e6b87493p@chr6:168251000..168251007, +
2.98e-60FFCP PHASE2:Hg19::chr13:99135278..99135298,-#_738dbeca791825a8bfc7bf79a4686739p@chr13:99135278..99135298, -
2.98e-60FFCP PHASE1:Hg19::chr13:99135278..99135298,-#_738dbeca791825a8bfc7bf79a4686739p@chr13:99135278..99135298, -
5.01e-55FFCP PHASE1:Hg19::chr3:69928371..69928385,+#_9e7c34dc89ca8430db3304ff1ca131b9p@chr3:69928371..69928385, +
5.01e-55FFCP PHASE2:Hg19::chr3:69928371..69928385,+#_9e7c34dc89ca8430db3304ff1ca131b9p@chr3:69928371..69928385, +
7.24e-55FFCP PHASE1:Hg19::chr14:87636652..87636657,-#_6f802fe891eead563f326121edb2fa7ep@chr14:87636652..87636657, -
7.24e-55FFCP PHASE2:Hg19::chr14:87636652..87636657,-#_6f802fe891eead563f326121edb2fa7ep@chr14:87636652..87636657, -
1.68e-53FFCP PHASE1:Hg19::chr2:235591286..235591298,+#_0c3c46f0da1ce2ff6eabcb2f1cc7805bp@chr2:235591286..235591298, +
1.68e-53FFCP PHASE2:Hg19::chr2:235591286..235591298,+#_0c3c46f0da1ce2ff6eabcb2f1cc7805bp@chr2:235591286..235591298, +
6.39e-53FFCP PHASE2:Hg19::chr16:84228961..84228982,+#_b1303650edf6c39795b77dad071e0f19p@chr16:84228961..84228982, +
6.39e-53FFCP PHASE2:Hg19::chr11:119217442..119217445,-#_b1303650edf6c39795b77dad071e0f19p5@MFRP, p6@C1QTNF5
6.39e-53FFCP PHASE1:Hg19::chr16:84228961..84228982,+#_b1303650edf6c39795b77dad071e0f19p@chr16:84228961..84228982, +
6.39e-53FFCP PHASE1:Hg19::chr11:119217442..119217445,-#_b1303650edf6c39795b77dad071e0f19p5@MFRP, p6@C1QTNF5
9.6e-51FFCP PHASE2:Hg19::chr21:36041264..36041274,+#_1f0aaca7966283ff9e09a5f68242dacdp3@CLIC6
9.6e-51FFCP PHASE1:Hg19::chr21:36041264..36041274,+#_1f0aaca7966283ff9e09a5f68242dacdp3@CLIC6
1.89e-50FFCP PHASE2:Hg19::chr11:75201755..75201762,-#_8b03ac4dc01fb86dc1fd3ebc20c3e030p7@GDPD5
1.89e-50FFCP PHASE1:Hg19::chr11:75201755..75201762,-#_8b03ac4dc01fb86dc1fd3ebc20c3e030p7@GDPD5
7.24e-50FFCP PHASE2:Hg19::chr11:119217421..119217435,-#_b587ad0e0dde8f789c2c9a3f4d87a749p4@MFRP, p5@C1QTNF5
7.24e-50FFCP PHASE1:Hg19::chr11:119217421..119217435,-#_b587ad0e0dde8f789c2c9a3f4d87a749p4@MFRP, p5@C1QTNF5
6.25e-45FFCP PHASE1:Hg19::chr17:932596..932605,-#_f109dc0b882c84cf04cff084a082001fp@chr17:932596..932605, -
6.25e-45FFCP PHASE2:Hg19::chr17:932596..932605,-#_f109dc0b882c84cf04cff084a082001fp@chr17:932596..932605, -
1.22e-44FFCP PHASE2:Hg19::chr17:932340..932343,-#_5ca01b21b34cdc7c2f420e0443028f07p@chr17:932340..932343, -
1.22e-44FFCP PHASE1:Hg19::chr20:52790691..52790695,-#_5ca01b21b34cdc7c2f420e0443028f07p5@CYP24A1
1.22e-44FFCP PHASE2:Hg19::chr20:52790691..52790695,-#_5ca01b21b34cdc7c2f420e0443028f07p5@CYP24A1
1.22e-44FFCP PHASE2:Hg19::chr22:38480132..38480159,-#_5ca01b21b34cdc7c2f420e0443028f07p1@SLC16A8
1.22e-44FFCP PHASE1:Hg19::chr22:38480132..38480159,-#_5ca01b21b34cdc7c2f420e0443028f07p1@SLC16A8
1.22e-44FFCP PHASE1:Hg19::chr17:932340..932343,-#_5ca01b21b34cdc7c2f420e0443028f07p@chr17:932340..932343, -
2.38e-44FFCP PHASE2:Hg19::chr3:98672197..98672201,+#_ed7449815d56ec8fa44bdf9cf7996648p@chr3:98672197..98672201, +
2.38e-44FFCP PHASE1:Hg19::chr3:98672197..98672201,+#_ed7449815d56ec8fa44bdf9cf7996648p@chr3:98672197..98672201, +
2.97e-44FFCP PHASE1:Hg19::chr3:183733654..183733680,-#_1d18547829452a762418ed36d84ba14dp@chr3:183733654..183733680, -
2.97e-44FFCP PHASE1:Hg19::chr9:127025189..127025200,+#_1d18547829452a762418ed36d84ba14dp1@ENST00000437461
2.97e-44FFCP PHASE2:Hg19::chr9:127025189..127025200,+#_1d18547829452a762418ed36d84ba14dp1@ENST00000437461
2.97e-44FFCP PHASE2:Hg19::chr3:183733654..183733680,-#_1d18547829452a762418ed36d84ba14dp@chr3:183733654..183733680, -
4.49e-44FFCP PHASE2:Hg19::chr9:140088882..140088898,-#_ffe9835dae763e27f31e654bd1f8b8ccp@chr9:140088882..140088898, -
4.49e-44FFCP PHASE1:Hg19::chr9:140088882..140088898,-#_ffe9835dae763e27f31e654bd1f8b8ccp@chr9:140088882..140088898, -
1.24e-43FFCP PHASE2:Hg19::chr14:28081776..28081788,+#_b089e87f63181a0c22bbc6f58ec0eab2p1@LOC100505967
1.24e-43FFCP PHASE1:Hg19::chr14:28081776..28081788,+#_b089e87f63181a0c22bbc6f58ec0eab2p1@LOC100505967
2.95e-43FFCP PHASE1:Hg19::chr2:45169172..45169177,+#_5e0541e63fdb7654a75937ac627c82e4p11@SIX3
2.95e-43FFCP PHASE2:Hg19::chr2:45169172..45169177,+#_5e0541e63fdb7654a75937ac627c82e4p11@SIX3
4.55e-43FFCP PHASE2:Hg19::chr5:33984786..33984820,-#_7a1420bd9530a8e6a96828e1779924fap2@SLC45A2
4.55e-43FFCP PHASE1:Hg19::chr5:33984786..33984820,-#_7a1420bd9530a8e6a96828e1779924fap2@SLC45A2
3.86e-41FFCP PHASE2:Hg19::chr16:68301840..68301845,+#_284f3b5298b729d683092b2ea5810e05p@chr16:68301840..68301845, +
3.86e-41FFCP PHASE1:Hg19::chr16:68301840..68301845,+#_284f3b5298b729d683092b2ea5810e05p@chr16:68301840..68301845, +
9.96e-41FFCP PHASE2:Hg19::chr19:49140255..49140268,-#_eca03f0f464ccb648a1cd6c5efb05684p9@DBP
9.96e-41FFCP PHASE1:Hg19::chr19:49140255..49140268,-#_eca03f0f464ccb648a1cd6c5efb05684p9@DBP
1.31e-40FFCP PHASE2:Hg19::chr12:52579447..52579461,-#_089f7e0805906cf545a13e0f0630f04cp6@KRT80
1.31e-40FFCP PHASE1:Hg19::chr12:52579447..52579461,-#_089f7e0805906cf545a13e0f0630f04cp6@KRT80
1.49e-40FFCP PHASE1:Hg19::chr4:23886471..23886501,-#_f2b853036e2549ea59de95d7e057a308p5@PPARGC1A
1.49e-40FFCP PHASE2:Hg19::chr4:23886471..23886501,-#_f2b853036e2549ea59de95d7e057a308p5@PPARGC1A
1.71e-40FFCP PHASE2:Hg19::chr11:119217318..119217346,-#_6d2f4c0f2057ad1a001180d547b059d0p2@MFRP
1.71e-40FFCP PHASE1:Hg19::chr11:119217318..119217346,-#_6d2f4c0f2057ad1a001180d547b059d0p2@MFRP
1.96e-40FFCP PHASE1:Hg19::chr11:119217405..119217420,-#_f5f00f9aa9fe151b72fe8c0501faa45ap3@C1QTNF5, p3@MFRP
1.96e-40FFCP PHASE2:Hg19::chr11:119217405..119217420,-#_f5f00f9aa9fe151b72fe8c0501faa45ap3@C1QTNF5, p3@MFRP
2.93e-40FFCP PHASE1:Hg19::chr8:144905532..144905541,-#_b8f457d18ced0a96ce4e6a46322a9d2dp6@PUF60
2.93e-40FFCP PHASE2:Hg19::chr8:144905532..144905541,-#_b8f457d18ced0a96ce4e6a46322a9d2dp6@PUF60
3.83e-40FFCP PHASE2:Hg19::chr2:45162900..45162914,-#_8e1c6721ba822edd0b660ff3e96c617bp1@ENST00000432125
3.83e-40FFCP PHASE1:Hg19::chr2:45162900..45162914,-#_8e1c6721ba822edd0b660ff3e96c617bp1@ENST00000432125
6.54e-40FFCP PHASE1:Hg19::chr9:73483992..73484003,-#_a4296ab48808ba3eb57cb7dbccc837cfp6@TRPM3
6.54e-40FFCP PHASE2:Hg19::chr9:73483992..73484003,-#_a4296ab48808ba3eb57cb7dbccc837cfp6@TRPM3
1.11e-38FFCP PHASE1:Hg19::chr11:67776077..67776088,+#_eddb6d9567ecce82446093f606cf9c41p5@ALDH3B1
1.11e-38FFCP PHASE2:Hg19::chr11:67776077..67776088,+#_eddb6d9567ecce82446093f606cf9c41p5@ALDH3B1










Property "Property value" (as page type) with input value "UBPROP:0000001 "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. 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 "The monolayer of pigmented epithelium covering the neural retina.[AAO]" xsd:string" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.

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