FF:10707-109H5: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:10707-109H5
|name=transitional cell carcinoma cell line:Hs 769.T, biol_rep1
|sample_id=10707
|rna_tube_id=109H5
|rna_box=109
|rna_position=H5
|sample...") |
No edit summary |
||
| Line 1: | Line 1: | ||
{{f5samples | {{f5samples | ||
|id=FF:10707-109H5 | |id=FF:10707-109H5 | ||
|name=transitional cell carcinoma cell line:Hs 769.T | |name=transitional cell carcinoma cell line:Hs 769.T | ||
|sample_id=10707 | |sample_id=10707 | ||
|rna_tube_id=109H5 | |rna_tube_id=109H5 | ||
| Line 20: | Line 20: | ||
|sample_ethnicity=B | |sample_ethnicity=B | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230=1. | |rna_od260/230=1.85 | ||
|rna_od260/280=2. | |rna_od260/280=2.08 | ||
|sample_cell_type=epithelial cell, transitional | |sample_cell_type=epithelial cell, transitional | ||
|sample_cell_line=Hs 769.T | |sample_cell_line=Hs 769.T | ||
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | |sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | ||
| Line 40: | Line 40: | ||
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:2671,DOID:305,DOID:4 | |ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:2671,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 | ||
| Line 67: | Line 66: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:58, 27 February 2012
| Name: | transitional cell carcinoma cell line:Hs 769.T |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
| Download raw sequence, BAM & CTSS | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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: CNhs11837This 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: CNhs11837This 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: CNhs11837
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)
0000255 (eukaryotic cell)
0000548 (animal cell)
DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2671 (transitional cell carcinoma)
305 (carcinoma)
4 (disease)
UBERON: Anatomy
0000061 (anatomical structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)
0005910 (transitional epithelium)
0005911 (endo-epithelium)
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
