FF:10646-109A7: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:10646-109A7
|name=squamous cell carcinoma cell line:JHUS-nk1, biol_rep1
|sample_id=10646
|rna_tube_id=109A7
|rna_box=109
|rna_position=A7
|sample_cel...") |
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{{f5samples | {{f5samples | ||
|id=FF:10646-109A7 | |id=FF:10646-109A7 | ||
|name=squamous cell carcinoma cell line:JHUS-nk1 | |name=squamous cell carcinoma cell line:JHUS-nk1 | ||
|sample_id=10646 | |sample_id=10646 | ||
|rna_tube_id=109A7 | |rna_tube_id=109A7 | ||
| Line 7: | Line 7: | ||
|rna_position=A7 | |rna_position=A7 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_catalog=RCB1558 | |sample_cell_catalog=RCB1558 | ||
|sample_company=RIKEN Bioresource centre | |sample_company=RIKEN Bioresource centre | ||
|rna_lot_number= | |rna_lot_number= | ||
| Line 20: | Line 20: | ||
|sample_ethnicity=J | |sample_ethnicity=J | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230=2 | |rna_od260/230=2 | ||
|rna_od260/280=2. | |rna_od260/280=2.09 | ||
|sample_cell_type=unclassifiable | |sample_cell_type=unclassifiable | ||
|sample_cell_line=JHUS-nk1 | |sample_cell_line=JHUS-nk1 | ||
|sample_collaboration=Yukio Nakamura (RIKEN BRC) | |sample_collaboration=Yukio Nakamura (RIKEN BRC) | ||
|sample_experimental_condition= | |sample_experimental_condition= | ||
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|rna_sample_type=total RNA | |rna_sample_type=total RNA | ||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | ||
|rna_weight_ug=118. | |rna_weight_ug=118.866 | ||
|rna_concentration=1.58488 | |rna_concentration=1.58488 | ||
|sample_note= | |sample_note= | ||
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|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:1749,DOID:305,DOID:4 | |ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:1749,DOID:305,DOID:4 | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0101120 | |fonse_cell_line=FF:0101120 | ||
|fonse_cell_line_closure=FF:0101120 | |fonse_cell_line_closure=FF:0101120 | ||
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|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:53, 27 February 2012
| Name: | squamous cell carcinoma cell line:JHUS-nk1 |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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| Download raw sequence, BAM & CTSS | ||||||||||||
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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>dataNo results for this sample
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
library id: CNhs11749This sample isn't target for the analysis
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
library id: CNhs11749This sample isn't target for the analysis
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>
library id: CNhs11749
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
{{{is_a}}}
part_of relathionship
{{{part_of}}}
has_quality relathionship
{{{has_quality}}}
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)
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
