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{{f5samples
{{f5samples
|id=FF:10617-108G5
|F5samples=
|name=
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000153,UBERON:0000161,UBERON:0000165,UBERON:0000166,UBERON:0000344,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000930,UBERON:0000974,UBERON:0001004,UBERON:0001007,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0003343,UBERON:0003729,UBERON:0004111,UBERON:0004119,UBERON:0004785,UBERON:0004923,UBERON:0005423,UBERON:0005434,UBERON:0007026
|sample_id=10617
|rna_tube_id=108G5
|rna_box=108
|rna_position=G5
|sample_cell_lot=
|sample_cell_catalog=RCB1017
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=gum
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=33
|sample_ethnicity=J
|rna_rin=
|rna_od260/230=2.09
|rna_od260/280=2.13
|sample_cell_type=unclassifiable
|sample_cell_line=T3M-1 Cl-10
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=oral squamous cell carcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=32.30253
|rna_concentration=1.19639
|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:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000153,UBERON:0000161,UBERON:0000165,UBERON:0000166,UBERON:0000344,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000930,UBERON:0000974,UBERON:0001004,UBERON:0001007,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0003343,UBERON:0003729,UBERON:0004111,UBERON:0004119,UBERON:0004785,UBERON:0004923,UBERON:0005423,UBERON:0005434,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=
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|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10617-108G5
|is_a=EFO:0002091;;FF:0000210;;FF:0102211
|is_a=EFO:0002091;;FF:0000210;;FF:0102211
|name=
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=
|profile_hcage=,,,IN_LIBRARIAN
|profile_rnaseq=
|profile_srnaseq=
|rna_box=108
|rna_catalog_number=
|rna_concentration=1.19639
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.09
|rna_od260/280=2.13
|rna_position=G5
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=108G5
|rna_weight_ug=32.30253
|sample_age=33
|sample_cell_catalog=RCB1017
|sample_cell_line=T3M-1 Cl-10
|sample_cell_lot=
|sample_cell_type=unclassifiable
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_company=RIKEN Bioresource centre
|sample_description=
|sample_dev_stage=
|sample_disease=oral squamous cell carcinoma
|sample_donor(cell lot)=
|sample_ethnicity=J
|sample_experimental_condition=
|sample_id=10617
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=gum
|top_motifs=
}}
}}

Revision as of 14:11, 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
tissuegum
dev stageNA
sexmale
age33
cell typeunclassifiable
cell lineT3M-1 Cl-10
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000344 (mucosa)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000930 (stomodeum)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003343 (mucosa of oral region)
0003729 (mouth mucosa)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004785 (respiratory system mucosa)
0004923 (organ component layer)
0005423 (developing anatomical structure)
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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