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{{f5samples
 
{{f5samples
|id=FF:10653-109B5
+
|F5samples=
|name=
+
|ancestors_in_anatomy_facet=UBERON:0000059,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000160,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001155,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026
|sample_id=10653
 
|rna_tube_id=109B5
 
|rna_box=109
 
|rna_position=B5
 
|sample_cell_lot=
 
|sample_cell_catalog=RCB1705
 
|sample_company=RIKEN Bioresource centre
 
|rna_lot_number=
 
|rna_catalog_number=
 
|sample_species=Human (Homo sapiens)
 
|sample_strain=
 
|sample_dev_stage=
 
|sample_tissue=colon
 
|sample_donor(cell lot)=
 
|sample_sex=female
 
|sample_age=52
 
|sample_ethnicity=J
 
|rna_rin=
 
|rna_od260/230=2.14
 
|rna_od260/280=2.09
 
|sample_cell_type=unclassifiable
 
|sample_cell_line=JHCA-ov
 
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
 
|sample_experimental_condition=
 
|sample_disease=colon carcinoma
 
|rna_sample_type=total RNA
 
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
 
|rna_weight_ug=185.4281
 
|rna_concentration=1.68571
 
|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: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:0000059,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000160,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001155,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026
 
 
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:3119,DOID:4
 
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:3119,DOID:4
|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:10653-109B5
 
|is_a=EFO:0002091;;FF:0000210;;FF:0100797
 
|is_a=EFO:0002091;;FF:0000210;;FF:0100797
 +
|name=
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 +
|profile_cagescan=
 +
|profile_hcage=,,,IN_LIBRARIAN
 +
|profile_rnaseq=
 +
|profile_srnaseq=
 +
|rna_box=109
 +
|rna_catalog_number=
 +
|rna_concentration=1.68571
 +
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
 +
|rna_lot_number=
 +
|rna_od260/230=2.14
 +
|rna_od260/280=2.09
 +
|rna_position=B5
 +
|rna_rin=
 +
|rna_sample_type=total RNA
 +
|rna_tube_id=109B5
 +
|rna_weight_ug=185.4281
 +
|sample_age=52
 +
|sample_cell_catalog=RCB1705
 +
|sample_cell_line=JHCA-ov
 +
|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=colon carcinoma
 +
|sample_donor(cell lot)=
 +
|sample_ethnicity=J
 +
|sample_experimental_condition=
 +
|sample_id=10653
 +
|sample_note=
 +
|sample_sex=female
 +
|sample_species=Human (Homo sapiens)
 +
|sample_strain=
 +
|sample_tissue=colon
 +
|top_motifs=
 
}}
 
}}

Revision as of 05:12, 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
tissuecolon
dev stageNA
sexfemale
age52
cell typeunclassifiable
cell lineJHCA-ov
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.
Analyst:NA

link to dataset.
data


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



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



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA


FANTOM5 (FF) ontology


Direct parent terms


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)
162 (cancer)
305 (carcinoma)
3119 (gastrointestinal system cancer)
4 (disease)

UBERON: Anatomy
0000059 (large intestine)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000160 (intestine)
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)
0001155 (colon)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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