FF:13052-139H1

Name:	MCF7 breast cancer cell line response to HRG
Species:	Human (Homo sapiens)
Library ID:	CNhs12439
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information
Sample information strain NA tissue breast dev stage NA sex female age NA cell type mammary gland epithelial cell cell line MCF7 company NA collaboration Mariko Okada Hatakeyama (RIKEN RCAI) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type NA extraction protocol (Details) Repurified by minelute

CAGE Accession numbers
Method Sample accession id CAGE  SAMD00021692 Library accession numbers Library id Method Exp. accession id Run accession id CNhs12439 CAGE DRX023353 DRR025728 DRR025729 DRR025730 Accession ID Hg19 Library id BAM CTSS CNhs12439 DRZ004153 DRZ004154 DRZ004155 DRZ005000 Accession ID Hg38 Library id BAM CTSS CNhs12439 DRZ008894 DRZ008895 DRZ008896 DRZ009741

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

RNA-Seq Accession numbers
Method Sample accession id sRNA-Seq  SAMD00021692 Library accession numbers Library id Method Exp. accession id Run accession id SRhi10064.TGACCA sRNA-Seq DRX037307 DRR041673 Accession ID Hg19 Library id BAM CTSS SRhi10064.TGACCA DRZ007315 Accession ID Hg38 Library id BAM CTSS SRhi10064.TGACCA

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: CNhs12439This 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: CNhs12439This 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: CNhs12439

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000447 human MCF7 breast cancer cell line 80min after HRG treatment 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)
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)
0000351 (80 minutes 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)
0000447 (human MCF7 breast cancer cell line 80min after HRG treatment 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