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|located_in=
|located_in=
|name=pigmented layer of retina
|name=pigmented layer of retina
|namespace=
|namespace=FANTOM
|obo_creation_date=
|obo_creation_date=
|part_of=
|part_of=

Latest revision as of 17:20, 12 September 2014

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<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: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<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:0001782 (pigmented 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
2.79e-195FFCP PHASE2:Hg19::chr1:147150847..147150854,-#_9f7dbf71f3f059a0b649bc64883f1acfp@chr1:147150847..147150854, -
2.79e-195FFCP PHASE1: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 PHASE2:Hg19::chr13:51913893..51913901,+#_18709429f3383a3d05e54b02e1c6a4b8p@chr13:51913893..51913901, +
8.98e-131FFCP PHASE1:Hg19::chr13:51913893..51913901,+#_18709429f3383a3d05e54b02e1c6a4b8p@chr13:51913893..51913901, +
3.48e-118FFCP PHASE1:Hg19::chr11:109990513..109990520,-#_c0f14d5c475472a051b78a26ec829852p@chr11:109990513..109990520, -
3.48e-118FFCP PHASE2: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 PHASE1:Hg19::chr11:61522844..61522875,+#_d2747888d77ce46c3775f0bd1488c9c9p2@C11orf9
7.95e-99FFCP PHASE2: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 PHASE1:Hg19::chr8:75898210..75898219,+#_df552b259893dd7ba36ce8fe6b1f3070p11@CRISPLD1
9.74e-88FFCP PHASE2: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 PHASE2:Hg19::chr13:51913819..51913838,+#_82143b06b3bec80f0dbf904fbc4963d4p1@SERPINE3
2.28e-85FFCP PHASE1:Hg19::chr13:51913819..51913838,+#_82143b06b3bec80f0dbf904fbc4963d4p1@SERPINE3
1.01e-74FFCP PHASE2:Hg19::chr3:69928426..69928436,+#_c5768543d2edab0842d00f1a4fe663b2p@chr3:69928426..69928436, +
1.01e-74FFCP PHASE1:Hg19::chr3:69928426..69928436,+#_c5768543d2edab0842d00f1a4fe663b2p@chr3:69928426..69928436, +
1.29e-74FFCP PHASE2:Hg19::chr3:69928404..69928418,+#_90461782acdc02205385827845cd0df0p@chr3:69928404..69928418, +
1.29e-74FFCP PHASE1:Hg19::chr3:69928404..69928418,+#_90461782acdc02205385827845cd0df0p@chr3:69928404..69928418, +
2.14e-74FFCP PHASE1:Hg19::chr6:168250971..168250985,+#_1cb67501a155134dc7b0a32941ccdd62p@chr6:168250971..168250985, +
2.14e-74FFCP PHASE2:Hg19::chr6:168250971..168250985,+#_1cb67501a155134dc7b0a32941ccdd62p@chr6:168250971..168250985, +
2.14e-74FFCP PHASE1:Hg19::chr22:37633537..37633546,-#_1cb67501a155134dc7b0a32941ccdd62p@chr22:37633537..37633546, -
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,+#_2e92c2118ab60fa49ffbc03677e8bfcfp@chr1:43533230..43533270, +
1.54e-66FFCP PHASE1:Hg19::chr21:36041275..36041282,+#_d74bba9507044d4ca1674286d61af093p5@CLIC6
1.54e-66FFCP PHASE2: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 PHASE1:Hg19::chr13:99135278..99135298,-#_738dbeca791825a8bfc7bf79a4686739p@chr13:99135278..99135298, -
2.98e-60FFCP PHASE2:Hg19::chr13:99135278..99135298,-#_738dbeca791825a8bfc7bf79a4686739p@chr13:99135278..99135298, -
5.01e-55FFCP PHASE2:Hg19::chr3:69928371..69928385,+#_9e7c34dc89ca8430db3304ff1ca131b9p@chr3:69928371..69928385, +
5.01e-55FFCP PHASE1: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 PHASE1: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::chr11:119217442..119217445,-#_b1303650edf6c39795b77dad071e0f19p5@MFRP, p6@C1QTNF5
9.6e-51FFCP PHASE1:Hg19::chr21:36041264..36041274,+#_1f0aaca7966283ff9e09a5f68242dacdp3@CLIC6
9.6e-51FFCP PHASE2: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 PHASE2:Hg19::chr17:932596..932605,-#_f109dc0b882c84cf04cff084a082001fp@chr17:932596..932605, -
6.25e-45FFCP PHASE1:Hg19::chr17:932596..932605,-#_f109dc0b882c84cf04cff084a082001fp@chr17:932596..932605, -
1.22e-44FFCP PHASE2:Hg19::chr20:52790691..52790695,-#_5ca01b21b34cdc7c2f420e0443028f07p5@CYP24A1
1.22e-44FFCP PHASE1:Hg19::chr22:38480132..38480159,-#_5ca01b21b34cdc7c2f420e0443028f07p1@SLC16A8
1.22e-44FFCP PHASE2:Hg19::chr22:38480132..38480159,-#_5ca01b21b34cdc7c2f420e0443028f07p1@SLC16A8
1.22e-44FFCP PHASE2:Hg19::chr17:932340..932343,-#_5ca01b21b34cdc7c2f420e0443028f07p@chr17:932340..932343, -
1.22e-44FFCP PHASE1:Hg19::chr17:932340..932343,-#_5ca01b21b34cdc7c2f420e0443028f07p@chr17:932340..932343, -
1.22e-44FFCP PHASE1:Hg19::chr20:52790691..52790695,-#_5ca01b21b34cdc7c2f420e0443028f07p5@CYP24A1
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 PHASE2:Hg19::chr3:183733654..183733680,-#_1d18547829452a762418ed36d84ba14dp@chr3:183733654..183733680, -
2.97e-44FFCP PHASE2:Hg19::chr9:127025189..127025200,+#_1d18547829452a762418ed36d84ba14dp1@ENST00000437461
2.97e-44FFCP PHASE1:Hg19::chr3:183733654..183733680,-#_1d18547829452a762418ed36d84ba14dp@chr3:183733654..183733680, -
2.97e-44FFCP PHASE1:Hg19::chr9:127025189..127025200,+#_1d18547829452a762418ed36d84ba14dp1@ENST00000437461
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 PHASE1:Hg19::chr14:28081776..28081788,+#_b089e87f63181a0c22bbc6f58ec0eab2p1@LOC100505967
1.24e-43FFCP PHASE2:Hg19::chr14:28081776..28081788,+#_b089e87f63181a0c22bbc6f58ec0eab2p1@LOC100505967
2.95e-43FFCP PHASE2:Hg19::chr2:45169172..45169177,+#_5e0541e63fdb7654a75937ac627c82e4p11@SIX3
2.95e-43FFCP PHASE1:Hg19::chr2:45169172..45169177,+#_5e0541e63fdb7654a75937ac627c82e4p11@SIX3
4.55e-43FFCP PHASE1:Hg19::chr5:33984786..33984820,-#_7a1420bd9530a8e6a96828e1779924fap2@SLC45A2
4.55e-43FFCP PHASE2: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 PHASE2:Hg19::chr11:119217405..119217420,-#_f5f00f9aa9fe151b72fe8c0501faa45ap3@C1QTNF5, p3@MFRP
1.96e-40FFCP PHASE1:Hg19::chr11:119217405..119217420,-#_f5f00f9aa9fe151b72fe8c0501faa45ap3@C1QTNF5, p3@MFRP
2.93e-40FFCP PHASE2:Hg19::chr8:144905532..144905541,-#_b8f457d18ced0a96ce4e6a46322a9d2dp6@PUF60
2.93e-40FFCP PHASE1: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 PHASE2:Hg19::chr9:73483992..73484003,-#_a4296ab48808ba3eb57cb7dbccc837cfp6@TRPM3
6.54e-40FFCP PHASE1:Hg19::chr9:73483992..73484003,-#_a4296ab48808ba3eb57cb7dbccc837cfp6@TRPM3
1.11e-38FFCP PHASE2:Hg19::chr11:67776077..67776088,+#_eddb6d9567ecce82446093f606cf9c41p5@ALDH3B1
1.11e-38FFCP PHASE1: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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