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{{f5samples
{{f5samples
|id=FF:10733-110B4
|F5samples=
|name=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005423,UBERON:0006562,UBERON:0007026
|sample_id=10733
|rna_tube_id=110B4
|rna_box=110
|rna_position=B4
|sample_cell_lot=
|sample_cell_catalog=HTB-43
|sample_company=ATCC
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=pharynx
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=56
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=2.11
|rna_od260/280=2.07
|sample_cell_type=unclassifiable
|sample_cell_line=FaDu
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=pharyngeal carcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=79.37078
|rna_concentration=1.68874
|sample_note=
|profile_hcage=,,,IN_LIBRARIAN
|profile_cagescan=
|profile_srnaseq=
|profile_rnaseq=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005423,UBERON:0006562,UBERON:0007026
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:1749,DOID:305,DOID:4,DOID:7
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:1749,DOID:305,DOID:4,DOID:7
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 34:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10733-110B4
|is_a=EFO:0002091;;FF:0000210;;FF:0103233
|is_a=EFO:0002091;;FF:0000210;;FF:0103233
|name=
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=
|profile_hcage=,,,IN_LIBRARIAN
|profile_rnaseq=
|profile_srnaseq=
|rna_box=110
|rna_catalog_number=
|rna_concentration=1.68874
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.11
|rna_od260/280=2.07
|rna_position=B4
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=110B4
|rna_weight_ug=79.37078
|sample_age=56
|sample_cell_catalog=HTB-43
|sample_cell_line=FaDu
|sample_cell_lot=
|sample_cell_type=unclassifiable
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=ATCC
|sample_description=
|sample_dev_stage=
|sample_disease=pharyngeal carcinoma
|sample_donor(cell lot)=
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10733
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=pharynx
|top_motifs=
}}
}}

Revision as of 14:13, 21 March 2012


Name:
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepharynx
dev stageNA
sexmale
age56
cell typeunclassifiable
cell lineFaDu
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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>data

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



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



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>


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)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
1749 (squamous cell carcinoma)
305 (carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0006562 (pharynx)
0007026 (primitive gut)

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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