FF:10054-101G9

Name:	eye, fetal, donor1
Species:	Human (Homo sapiens)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

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Sample information strain NA tissue eye dev stage 36 weeks fetus sex female age NA cell type CELL MIXTURE - tissue sample cell line NA company Biochain collaboration FANTOM5 OSC CORE (contact: Al Forrest) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number B210179 catalog number Cat:RtHFN: Whole Eye sample type total RNA extraction protocol (Details) OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

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CollapseHg19 BAM CTSS [{{{hg19bam}}} download] [{{{hg19ctss}}} donwload] CollapseHg38 BAM CTSS [{{{hg38bam}}} download] [{{{hg38ctss}}} 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>data

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MCL coexpression id	Coexpression_dpi_cluster_scores_median_value
C40-eye-retina-Lens-pineal-tongue-retinoblastoma-small	1.057
C59-Smooth-Fibroblast-Mesenchymal-tenocyte-Ewing-skin-hepatic	0.759
C286-cerebellum-occipital-optic-parietal-globus-caudate-medial	0.724
C172-chorionic-skeletal-tongue-amniotic-liver-gastrointestinal-Pericytes	0.642
C292-Mesenchymal-skin-umbilical-Adipocyte-mesenchymal-Chondrocyte-skeletal	0.607
C252-hepatic-Olfactory-sacrococcigeal-leiomyoma-normal-Synoviocyte-glioblastoma	0.542
C288-Chondrocyte-Renal-Pericytes-Fibroblast-aorta-Smooth-Meningeal	0.513
C227-chorionic-amniotic-Mesenchymal-Placental-gastric-diaphragm-tongue	0.372
C41-retina-eye-medulla-Retinal-medulloblastoma-kidney-pineal	0.304
C284-parietal-occipital-medial-temporal-olfactory-locus-hippocampus	0.286

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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: CNhs11762

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MA0099.2		1.01e-20
MA0159.1		1.03e-1
MA0156.1		1.14e-12
MA0059.1		1.15e-2
MA0125.1		1.17e-1
Jaspar motif	Logo	p-value

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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: CNhs11762

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114		1.03e-1
7		1.04e-1
61		1.04e-2
123		1.07e-2
70		1.10e-1
Novel motif	Logo	p-value

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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: CNhs11762

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000004 tissue sample
FF:0000210 human sample
FF:0010054 human eye - fetal 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

UBERON: Anatomy
0000020 (sense organ)
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000970 (eye)
0001032 (sensory system)
0001062 (anatomical entity)
0002104 (visual system)
0004456 (entire sense organ system)

FF: FANTOM5
NA

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