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{{f5samples
{{f5samples
|id=FF:10630-108H9
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0001282,UBERON:0002394,UBERON:0000058,UBERON:0001007,UBERON:0000064,UBERON:0004119,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0009842,UBERON:0000353,UBERON:0003704,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0003928,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0001280,UBERON:0001171,UBERON:0004647,UBERON:0002294,UBERON:0001173,UBERON:0001172,UBERON:0002330,UBERON:0000916,UBERON:0002423
|name=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000181,CL:0000417,CL:0000668,CL:0000412,CL:0000255,CL:0000182
|sample_id=10630
|ancestors_in_disease_facet=DOID:4,DOID:162,DOID:14566,DOID:0050687,DOID:7,DOID:305
|rna_tube_id=108H9
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001,FF:0100297,FF:0101120,FF:0100224,FF:0100578,FF:0102842
|rna_box=108
|comment=
|rna_position=H9
|created_by=
|sample_cell_lot=
|creation_date=
|sample_cell_catalog=RCB1293
|def=
|sample_company=RIKEN Bioresource centre
|f5samples=
|rna_lot_number=
|ffid_belonging_in_development=CL:0000134,CL:0000223,UBERON:0001041,UBERON:0002532,UBERON:0006595,UBERON:0003104,UBERON:0004161,UBERON:0009497,UBERON:0010316
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=liver
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=unknown
|sample_ethnicity=J
|rna_rin=
|rna_od260/230=1.95
|rna_od260/280=2.06
|sample_cell_type=duct cell, bile duct
|sample_cell_line=SSP-25
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=cholangiocellular carcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=16.97546
|rna_concentration=0.36118
|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_anatomy_facet=UBERON:0000015,UBERON:0000025,UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000077,UBERON:0000119,UBERON:0000353,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001171,UBERON:0001172,UBERON:0001173,UBERON:0001280,UBERON:0001282,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002294,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002394,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003104,UBERON:0003704,UBERON:0003894,UBERON:0003914,UBERON:0003928,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004647,UBERON:0004912,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0005911,UBERON:0006235,UBERON:0006925,UBERON:0007026,UBERON:0008835,UBERON:0008836,UBERON:0009142
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:4,DOID:7
|sample_description=
|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=
|has_quality=
|id=FF:10630-108H9
|is_a=EFO:0002091;;FF:0000210;;FF:0102842
|is_obsolete=
|name=
|namespace=FANTOM5
|part_of=
|profile_cagescan=
|profile_hcage=,,,IN_LIBRARIAN
|profile_rnaseq=
|profile_srnaseq=
|rna_box=108
|rna_catalog_number=
|rna_concentration=0.36118
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.95
|rna_od260/280=2.06
|rna_position=H9
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=108H9
|rna_weight_ug=16.97546
|sample_age=unknown
|sample_cell_catalog=RCB1293
|sample_cell_line=SSP-25
|sample_cell_lot=
|sample_cell_type=duct cell, bile duct
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_company=RIKEN Bioresource centre
|sample_description=
|sample_dev_stage=
|sample_disease=cholangiocellular carcinoma
|sample_donor(cell lot)=
|sample_ethnicity=J
|sample_experimental_condition=
|sample_id=10630
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=liver
|top_motifs=
|top_motifs=
|xref=
}}
}}

Latest revision as of 19:30, 9 July 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
tissueliver
dev stageNA
sexfemale
ageunknown
cell typeduct cell, bile duct
cell lineSSP-25
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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000181 (metabolising cell)
0000417 (endopolyploid cell)
0000668 (parenchymal cell)
0000412 (polyploid cell)
0000255 (eukaryotic cell)
0000182 (hepatocyte)

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

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0001282 (intralobular bile duct)
0002394 (bile duct)
0000058 (duct)
0001007 (digestive system)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0009842 (acinus)
0000353 (parenchyma)
0003704 (intrahepatic bile duct)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0003928 (digestive system duct)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0001280 (liver parenchyma)
0001171 (portal lobule)
0004647 (liver lobule)
0002294 (biliary system)
0001173 (biliary tree)
0001172 (hepatic acinus)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial cell line sample)
0100224 (liver cell line sample)
0100578 (hepatoma cell line sample)
0102842 (cholangioma cell 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
CL:0000134 (mesenchymal cell)
CL:0000223 (endodermal cell)
UBERON:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)

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