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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<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











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.