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{{f5samples
 
{{f5samples
|id=FF:10640-109A1
+
|F5samples=
|name=
+
|ancestors_in_anatomy_facet=
|sample_id=10640
 
|rna_tube_id=109A1
 
|rna_box=109
 
|rna_position=A1
 
|sample_cell_lot=
 
|sample_cell_catalog=RCB1544
 
|sample_company=RIKEN Bioresource centre
 
|rna_lot_number=
 
|rna_catalog_number=
 
|sample_species=Human (Homo sapiens)
 
|sample_strain=
 
|sample_dev_stage=
 
|sample_tissue=uterus
 
|sample_donor(cell lot)=
 
|sample_sex=female
 
|sample_age=56
 
|sample_ethnicity=J
 
|rna_rin=
 
|rna_od260/230=2.16
 
|rna_od260/280=2.1
 
|sample_cell_type=unclassifiable
 
|sample_cell_line=JHUAS-1
 
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
 
|sample_experimental_condition=
 
|sample_disease=adenosquamous carcinoma
 
|rna_sample_type=total RNA
 
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
 
|rna_weight_ug=100.6335
 
|rna_concentration=1.34178
 
|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=
 
 
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:1749,DOID:299,DOID:305,DOID:4,DOID:4830
 
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:1749,DOID:299,DOID:305,DOID:4,DOID:4830
|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:10640-109A1
 
|is_a=EFO:0002091;;FF:0000210;;FF:0103849
 
|is_a=EFO:0002091;;FF:0000210;;FF:0103849
 +
|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=1.34178
 +
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
 +
|rna_lot_number=
 +
|rna_od260/230=2.16
 +
|rna_od260/280=2.1
 +
|rna_position=A1
 +
|rna_rin=
 +
|rna_sample_type=total RNA
 +
|rna_tube_id=109A1
 +
|rna_weight_ug=100.6335
 +
|sample_age=56
 +
|sample_cell_catalog=RCB1544
 +
|sample_cell_line=JHUAS-1
 +
|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=adenosquamous carcinoma
 +
|sample_donor(cell lot)=
 +
|sample_ethnicity=J
 +
|sample_experimental_condition=
 +
|sample_id=10640
 +
|sample_note=
 +
|sample_sex=female
 +
|sample_species=Human (Homo sapiens)
 +
|sample_strain=
 +
|sample_tissue=uterus
 +
|top_motifs=
 
}}
 
}}

Revision as of 05:11, 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
tissueuterus
dev stageNA
sexfemale
age56
cell typeunclassifiable
cell lineJHUAS-1
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)
299 (adenocarcinoma)
305 (carcinoma)
4 (disease)
4830 (adenosquamous carcinoma)

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