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(Created page with "{{f5samples |id=FF:13164-141B5 |name=MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep3 |sample_id=13164 |rna_tube_id=141B5 |rna_box=141 |rna_position=B...")
 
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|sample_ethnicity=
 
|sample_ethnicity=
 
|rna_rin=
 
|rna_rin=
|rna_od260/230=1.75000
+
|rna_od260/230=1.75
|rna_od260/280=2.03000
+
|rna_od260/280=2.03
 
|sample_cell_type=mammary gland epithelial cell
 
|sample_cell_type=mammary gland epithelial cell
 
|sample_cell_line=MCF7
 
|sample_cell_line=MCF7
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|rna_sample_type=
 
|rna_sample_type=
 
|rna_extraction_protocol=Repurified by minelute
 
|rna_extraction_protocol=Repurified by minelute
|rna_weight_ug=6.69340
+
|rna_weight_ug=6.69
|rna_concentration=0.66934
+
|rna_concentration=0.67
 
|sample_note=
 
|sample_note=
 
|profile_hcage=CNhs12704,LSID953,release011,COMPLETED
 
|profile_hcage=CNhs12704,LSID953,release011,COMPLETED
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|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=
 
|sample_description=
 
 
|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=EFO:0000369,FF:0000330,FF:0000427,FF:13164-141B5
 
|fonse_treatment=EFO:0000369,FF:0000330,FF:0000427,FF:13164-141B5
 
|fonse_treatment_closure=EFO:0000369,FF:0000330,FF:0000427,FF:13164-141B5
 
|fonse_treatment_closure=EFO:0000369,FF:0000330,FF:0000427,FF:13164-141B5
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|top_motifs=
 
}}
 
}}

Revision as of 08:42, 27 February 2012


Name:MCF7 breast cancer cell line response to EGF1, 00hr15min, biol_rep3
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.
Analyst:NA

link to dataset.
data
No 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: CNhs12704This 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: CNhs12704This 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: CNhs12704


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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

link to source data
data

NA