Personal tools

FF:13111-140E6: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021749
|accession_numbers=CAGE;DRX022936;DRR025275;DRZ003700;DRZ004583;DRZ008441;DRZ009324
|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:0000012,CL:0000063,CL:0000066,CL:0000004,CL:0000255
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
|ancestors_in_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:14566,DOID:0050687,DOID:7,DOID:5093,DOID:305,DOID:299,DOID:1612
|ancestors_in_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:14566,DOID:0050687,DOID:7,DOID:5093,DOID:305,DOID:299,DOID:1612
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001,FF:0000350,FF:0000364,FF:0000330,FF:0100093,FF:0100297,FF:0101912,FF:0101120,FF:0100816,FF:0100167,FF:0100356,FF:0000440
|comment=
|comment=
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|donor= biol_rep2
|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 34: Line 40:
|fonse_treatment_closure=EFO:0000369,FF:0000330,FF:0000440,FF:13111-140E6
|fonse_treatment_closure=EFO:0000369,FF:0000330,FF:0000440,FF:13111-140E6
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520EGF1%252c%252007hr%252c%2520biol_rep2.CNhs12490.13111-140E6.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520EGF1%252c%252007hr%252c%2520biol_rep2.CNhs12490.13111-140E6.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520EGF1%252c%252007hr%252c%2520biol_rep2.CNhs12490.13111-140E6.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%2520EGF1%252c%252007hr%252c%2520biol_rep2.CNhs12490.13111-140E6.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%2520EGF1%252c%252007hr%252c%2520biol_rep2.CNhs12490.13111-140E6.hg38.nobarcode.ctss.bed.gz
|id=FF:13111-140E6
|id=FF:13111-140E6
|is_a=EFO:0002091;;FF:0000440
|is_a=EFO:0002091;;FF:0000440
|is_obsolete=
|is_obsolete=
|name=MCF7 breast cancer cell line response to EGF1, 07hr, biol_rep2
|library_id=CNhs12490
|library_id_phase_based=2:CNhs12490
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;13111
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;13111
|name=MCF7 breast cancer cell line response to EGF1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs12490,LSID916,release011,COMPLETED
|profile_hcage=CNhs12490,LSID916,release011,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|rna_box=140
|rna_box=140
Line 54: Line 71:
|rna_rin=
|rna_rin=
|rna_sample_type=
|rna_sample_type=
|rna_tube_id=140E6
|rna_tube_id=1.40E+08
|rna_weight_ug=7.65
|rna_weight_ug=7.65
|sample_age=
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=MCF7
|sample_cell_line=MCF7
Line 75: Line 93:
|sample_strain=
|sample_strain=
|sample_tissue=breast
|sample_tissue=breast
|time= 07hr
|timecourse=MCF7_response_to_EGF
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:13111-140E6;search_select_hide=table117:FF:13111-140E6
}}
}}

Latest revision as of 18:51, 4 June 2020


Name:MCF7 breast cancer cell line response to EGF1
Species:Human (Homo sapiens)
Library ID:CNhs12490
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  SAMD00021749
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12490 CAGE DRX022936 DRR025275
Accession ID Hg19

Library idBAMCTSS
CNhs12490 DRZ003700 DRZ004583
Accession ID Hg38

Library idBAMCTSS
CNhs12490 DRZ008441 DRZ009324
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: CNhs12490This 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: CNhs12490This 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: CNhs12490


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)
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)
0000364 (7 hr sample)
0000330 (EGF1 treatment sample)
0100093 (MCF-7 cell 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)
0000440 (human MCF7 breast cancer cell line 7h after EGF1 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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:13111-140E6&oldid=4577536"