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{{f5samples
 
{{f5samples
 +
|DRA_sample_Accession=CAGE@SAMD00021699
 +
|accession_numbers=CAGE;DRX023360;DRR025749,DRR025750,DRR025751;DRZ004174,DRZ004175,DRZ004176;DRZ005007;DRZ008915,DRZ008916,DRZ008917;DRZ009748
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000310,UBERON:0002100,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0001062,UBERON:0009569,UBERON:0001443,UBERON:0000915
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000310,UBERON:0002100,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0001062,UBERON:0009569,UBERON:0001443,UBERON:0000915
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
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|creation_date=
 
|creation_date=
 
|data_phase=2
 
|data_phase=2
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|datafreeze_phase=2
 
|def=
 
|def=
 +
|donor= biol_rep1
 
|fonse_cell_line=FF:0100816,FF:0101120
 
|fonse_cell_line=FF:0100816,FF:0101120
 
|fonse_cell_line_closure=FF:0100816,FF:0101120
 
|fonse_cell_line_closure=FF:0100816,FF:0101120
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|fonse_treatment_closure=EFO:0000369,FF:0000331,FF:0000454,FF:13059-139H8
 
|fonse_treatment_closure=EFO:0000369,FF:0000331,FF:0000454,FF:13059-139H8
 
|has_quality=
 
|has_quality=
 +
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520HRG%252c%252005hr%252c%2520biol_rep1.CNhs12446.13059-139H8.hg19.nobarcode.bam
 +
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520HRG%252c%252005hr%252c%2520biol_rep1.CNhs12446.13059-139H8.hg19.ctss.bed.gz
 +
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520HRG%252c%252005hr%252c%2520biol_rep1.CNhs12446.13059-139H8.hg19.nobarcode.rdna.fa.gz
 +
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520HRG%252c%252005hr%252c%2520biol_rep1.CNhs12446.13059-139H8.hg38.nobarcode.bam
 +
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520HRG%252c%252005hr%252c%2520biol_rep1.CNhs12446.13059-139H8.hg38.nobarcode.ctss.bed.gz
 
|id=FF:13059-139H8
 
|id=FF:13059-139H8
 
|is_a=EFO:0002091;;FF:0000454
 
|is_a=EFO:0002091;;FF:0000454
 
|is_obsolete=
 
|is_obsolete=
 +
|library_id=CNhs12446
 
|library_id_phase_based=2:CNhs12446
 
|library_id_phase_based=2:CNhs12446
−
|name=MCF7 breast cancer cell line response to HRG, 05hr, biol_rep1
+
|microRNAs=
 +
|microRNAs_nn=
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|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;13059
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;13059
 +
|name=MCF7 breast cancer cell line response to HRG
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 
|profile_cagescan=,,,
 
|profile_cagescan=,,,
 
|profile_hcage=CNhs12446,LSID915,release011,COMPLETED
 
|profile_hcage=CNhs12446,LSID915,release011,COMPLETED
−
|profile_rnaseq=,,,
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|profile_rnaseq=
 
|profile_srnaseq=,,,
 
|profile_srnaseq=,,,
 
|rna_box=139
 
|rna_box=139
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|sample_strain=
 
|sample_strain=
 
|sample_tissue=breast
 
|sample_tissue=breast
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|time= 05hr
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|timecourse=MCF7_response_to_HRG
 
|top_motifs=
 
|top_motifs=
 
|xref=
 
|xref=
 +
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:13059-139H8;search_select_hide=table117:FF:13059-139H8
 
}}
 
}}

Latest revision as of 09:50, 4 June 2020


Name:MCF7 breast cancer cell line response to HRG
Species:Human (Homo sapiens)
Library ID:CNhs12446
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebreast
dev stageNA
sexfemale
ageNA
cell typemammary gland epithelial cell
cell lineMCF7
companyNA
collaborationMariko Okada Hatakeyama (RIKEN RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)Repurified by minelute

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021699
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12446 CAGE DRX023360 DRR025749
DRR025750
DRR025751
Accession ID Hg19

Library idBAMCTSS
CNhs12446 DRZ004174
DRZ004175
DRZ004176
 DRZ005007
Accession ID Hg38

Library idBAMCTSS
CNhs12446 DRZ008915
DRZ008916
DRZ008917
 DRZ009748
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.
Analyst:NA

link to dataset.
dataNo results for this sample

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data no result for this sample


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

JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data
library id: CNhs12446This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data
library id: CNhs12446This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs12446


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
7 (disease of anatomical entity)
5093 (thoracic cancer)
305 (carcinoma)
299 (adenocarcinoma)
1612 (breast cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000310 (breast)
0002100 (trunk)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0009569 (subdivision of trunk)
0001443 (chest)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000350 (experimentally modified sample)
0000362 (5 hr sample)
0100093 (MCF-7 cell sample)
0000331 (HRG treatment sample)
0100297 (carcinoma cell line sample)
0101912 (breast adenocarcinoma cell line sample)
0101120 (epithelial cell line sample)
0100816 (breast cell line sample)
0100167 (adenocarcinoma cell line sample)
0100356 (breast cancer cell line sample)
0000454 (human MCF7 breast cancer cell line 5h after HRG treatment sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data
NA

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