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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005015
|DRA_sample_Accession=CAGE@SAMD00005015
|accession_numbers=CAGE;DRX008654;DRR009526;DRZ000951;DRZ002336
|accession_numbers=CAGE;DRX008654;DRR009526;DRZ000951;DRZ002336;DRZ012301;DRZ013686
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000970,UBERON:0001797,UBERON:0000019,UBERON:0002384,UBERON:0000033,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0000466,UBERON:0000047,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0001444,UBERON:0002553,UBERON:0000477,UBERON:0000463,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0002203,UBERON:0003566,UBERON:0006312,UBERON:0006311,UBERON:0001032,UBERON:0002049,UBERON:0002200,UBERON:0006876,UBERON:0000464,UBERON:0010317,UBERON:0007798,UBERON:0004088,UBERON:0000153,UBERON:0007811,UBERON:0004535,UBERON:0002104,UBERON:0001802,UBERON:0004456,UBERON:0001456,UBERON:0001798,UBERON:0005606,UBERON:0001799,UBERON:0010230,UBERON:0001009
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000970,UBERON:0001797,UBERON:0000019,UBERON:0002384,UBERON:0000033,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0000466,UBERON:0000047,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0001444,UBERON:0002553,UBERON:0000477,UBERON:0000463,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0002203,UBERON:0003566,UBERON:0006312,UBERON:0006311,UBERON:0001032,UBERON:0002049,UBERON:0002200,UBERON:0006876,UBERON:0000464,UBERON:0010317,UBERON:0007798,UBERON:0004088,UBERON:0000153,UBERON:0007811,UBERON:0004535,UBERON:0002104,UBERON:0001802,UBERON:0004456,UBERON:0001456,UBERON:0001798,UBERON:0005606,UBERON:0001799,UBERON:0010230,UBERON:0001009
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=1
|data_phase=2
|datafreeze_phase=1
|datafreeze_phase=2
|def=
|def=
|fonse_cell_line=
|fonse_cell_line=
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/eye%2520-%2520vitreous%2520humor%252c%2520donor1.CNhs13440.10268-104D7.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/eye%2520-%2520vitreous%2520humor%252c%2520donor1.CNhs13440.10268-104D7.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/eye%2520-%2520vitreous%2520humor%252c%2520donor1.CNhs13440.10268-104D7.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/eye%2520-%2520vitreous%2520humor%252c%2520donor1.CNhs13440.10268-104D7.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/eye%2520-%2520vitreous%2520humor%252c%2520donor1.CNhs13440.10268-104D7.hg38.nobarcode.ctss.bed.gz
|id=FF:10268-104D7
|id=FF:10268-104D7
|is_a=EFO:0002091;;FF:0011157
|is_a=EFO:0002091;;FF:0011157
|is_obsolete=
|is_obsolete=
|library_id=CNhs13440
|library_id=CNhs13440
|library_id_phase_based=1:CNhs13440
|library_id_phase_based=2:CNhs13440
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10268
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10268
|name=eye - vitreous humor, donor1
|name=eye - vitreous humor, donor1
|namespace=
|namespace=
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|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs13440,LSID1024,release012,COMPLETED
|profile_hcage=CNhs13440,LSID1024,release012,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|rna_box=104
|rna_box=104
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|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10268-104D7;search_select_hide=table117:FF:10268-104D7
}}
}}

Latest revision as of 13:57, 3 June 2020


Name:eye - vitreous humor, donor1
Species:Human (Homo sapiens)
Library ID:CNhs13440
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueeye - vitreous humor
dev stageNA
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationAlessandro Bonetti
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1-Ey2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005015
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13440 CAGE DRX008654 DRR009526
Accession ID Hg19

Library idBAMCTSS
CNhs13440 DRZ000951 DRZ002336
Accession ID Hg38

Library idBAMCTSS
CNhs13440 DRZ012301 DRZ013686
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload





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

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: CNhs13440This 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: CNhs13440This 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: CNhs13440


FANTOM5 (FF) ontology

Direct parent terms


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
0000468 (multi-cellular organism)
0007023 (adult organism)
0000970 (eye)
0001797 (vitreous humor)
0000019 (camera-type eye)
0002384 (connective tissue)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0000466 (immaterial anatomical entity)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0001444 (subdivision of head)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000463 (organism substance)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0002203 (vasculature of eye)
0003566 (head connective tissue)
0006312 (ocular refractive media)
0006311 (chamber of eyeball)
0001032 (sensory system)
0002049 (vasculature)
0002200 (vasculature of head)
0006876 (vasculature of organ)
0000464 (anatomical space)
0010317 (germ layer / neural crest derived structure)
0007798 (vascular system)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0004535 (cardiovascular system)
0002104 (visual system)
0001802 (posterior segment of eyeball)
0004456 (entire sense organ system)
0001456 (face)
0001798 (vitreous body)
0005606 (hyaloid cavity)
0001799 (vitreous chamber of eyeball)
0010230 (eyeball of camera-type eye)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011157 (human eye - vitreous humor 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

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