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{{f5samples
{{f5samples
|id=FF:13127-140G4
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000310,UBERON:0000465,UBERON:0000468,UBERON:0000475,UBERON:0000915,UBERON:0001062,UBERON:0001443,UBERON:0005482
|name=MCF7 breast cancer cell line response to HRG, 07hr, biol_rep2
|sample_id=13127
|rna_tube_id=140G4
|rna_box=140
|rna_position=G4
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=breast
|sample_donor(cell lot)=rep2
|sample_sex=female
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=1.6
|rna_od260/280=1.97
|sample_cell_type=mammary gland epithelial cell
|sample_cell_line=MCF7
|sample_collaboration=Mariko Okada Hatakeyama (RIKEN RCAI)
|sample_experimental_condition=MCF7 breast cancer cell line response to Heregulin
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=Repurified by minelute
|rna_weight_ug=9.06
|rna_concentration=0.91
|sample_note=
|profile_hcage=CNhs12666,LSID953,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000310,UBERON:0000465,UBERON:0000468,UBERON:0000475,UBERON:0000915,UBERON:0001062,UBERON:0001443,UBERON:0005482
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:1612,DOID:162,DOID:299,DOID:305,DOID:4,DOID:5093,DOID:7
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:1612,DOID:162,DOID:299,DOID:305,DOID:4,DOID:5093,DOID:7
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|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
Line 66: Line 33:
|fonse_treatment=EFO:0000369,FF:0000331,FF:0000456,FF:13127-140G4
|fonse_treatment=EFO:0000369,FF:0000331,FF:0000456,FF:13127-140G4
|fonse_treatment_closure=EFO:0000369,FF:0000331,FF:0000456,FF:13127-140G4
|fonse_treatment_closure=EFO:0000369,FF:0000331,FF:0000456,FF:13127-140G4
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:13127-140G4
|is_a=EFO:0002091;;FF:0000210;;FF:0000456
|is_a=EFO:0002091;;FF:0000210;;FF:0000456
|name=MCF7 breast cancer cell line response to HRG, 07hr, biol_rep2
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12666,LSID953,release011,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=140
|rna_catalog_number=
|rna_concentration=0.91
|rna_extraction_protocol=Repurified by minelute
|rna_lot_number=
|rna_od260/230=1.6
|rna_od260/280=1.97
|rna_position=G4
|rna_rin=
|rna_sample_type=
|rna_tube_id=140G4
|rna_weight_ug=9.06
|sample_age=
|sample_cell_catalog=
|sample_cell_line=MCF7
|sample_cell_lot=
|sample_cell_type=mammary gland epithelial cell
|sample_collaboration=Mariko Okada Hatakeyama (RIKEN RCAI)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=rep2
|sample_ethnicity=
|sample_experimental_condition=MCF7 breast cancer cell line response to Heregulin
|sample_id=13127
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=breast
|top_motifs=
}}
}}

Revision as of 15:26, 21 March 2012


Name:MCF7 breast cancer cell line response to HRG, 07hr, biol_rep2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM: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
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{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>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: CNhs12666This 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: CNhs12666This 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: CNhs12666


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

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

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

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

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

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