FF:13680-147E8

Name:	ARPE-19 EMT induced with TGF-beta and TNF-alpha, 24hr00min, biol_rep2
Species:	Human (Homo sapiens)
Library ID:	CNhs14536
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information strain UNDEFINED_STRAIN tissue UNDEFINED_TISSUE_TYPE dev stage UNDEFINED_DEV_STAGE sex male age NA cell type retinal pigment epithelial cell cell line ARPE-19 company NA collaboration Tokyo Medical and Dental University External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type total RNA extraction protocol (Details) NA

CAGE Accession numbers
Method Sample accession id CAGE  SAMD00022291 Library accession numbers Library id Method Exp. accession id Run accession id CNhs14536 CAGE DRX023460 DRR025855 Accession ID Hg19 Library id BAM CTSS CNhs14536 DRZ004280 DRZ005107 Accession ID Hg38 Library id BAM CTSS CNhs14536 DRZ009021 DRZ009848

Download raw sequence, BAM & CTSS
Hg19 Fasta BAM CTSS download download donwload Hg38 BAM CTSS download donwload

Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>dataNo results for this sample

Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

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JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: CNhs14536This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: CNhs14536This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs14536

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
FF:0000210 human sample
FF:0300100 ARPE-19 EMT induced with TGF-beta and TNF-alpha sample

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000325 (stuff accumulating cell)
0000147 (pigment cell)
0000255 (eukaryotic cell)
0000149 (visual pigment cell)
0002586 (retinal pigment epithelial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000966 (retina)
0000970 (eye)
0000019 (camera-type eye)
0000483 (epithelium)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0004923 (organ component layer)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0005388 (photoreceptor array)
0000020 (sense organ)
0010371 (ecto-epithelium)
0007625 (pigment epithelium of eye)
0001781 (layer of retina)
0001032 (sensory system)
0010317 (germ layer / neural crest derived structure)
0001782 (pigmented layer of retina)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002104 (visual system)
0001802 (posterior segment of eyeball)
0004456 (entire sense organ system)
0001456 (face)
0010230 (eyeball of camera-type eye)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0300100 (ARPE-19 EMT induced with TGF-beta and TNF-alpha sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA