FF:12180-129A2: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:12180-129A2
|name=Whole blood (ribopure), donor090309, donation2 (repurified)
|sample_id=12180
|rna_tube_id=129A2
|rna_box=129
|rna_position=A2
|samp...") |
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{{f5samples | {{f5samples | ||
|id=FF:12180-129A2 | |id=FF:12180-129A2 | ||
|name=Whole blood (ribopure), donor090309, donation2 | |name=Whole blood (ribopure), donor090309, donation2 | ||
|sample_id=12180 | |sample_id=12180 | ||
|rna_tube_id=129A2 | |rna_tube_id=129A2 | ||
| Line 20: | Line 20: | ||
|sample_ethnicity= | |sample_ethnicity= | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230=2. | |rna_od260/230=2.19 | ||
|rna_od260/280=1. | |rna_od260/280=1.94 | ||
|sample_cell_type=CELL MIXTURE - tissue sample | |sample_cell_type=CELL MIXTURE - tissue sample | ||
|sample_cell_line= | |sample_cell_line= | ||
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|sample_experimental_condition= | |sample_experimental_condition= | ||
|sample_disease= | |sample_disease= | ||
|rna_sample_type= | |rna_sample_type=total RNA | ||
|rna_extraction_protocol= | |rna_extraction_protocol= | ||
|rna_weight_ug=14. | |rna_weight_ug=14.3 | ||
|rna_concentration=1. | |rna_concentration=1.195 | ||
|sample_note= | |sample_note= | ||
|profile_hcage=CNhs11671,LSID808,release008,COMPLETED | |profile_hcage=CNhs11671,LSID808,release008,COMPLETED | ||
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|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|sample_description= | |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= | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:59, 27 February 2012
| Name: | Whole blood (ribopure), donor090309, donation2 |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| ExpandAdditional information |
|---|
| ExpandDownload 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>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
library id: CNhs11671
| MA0152.1 |  | 1.06e-1 |
| MA0060.1 |  | 1.06e-3 |
| MA0035.2 |  | 1.11e-5 |
| MA0153.1 |  | 1.22e-1 |
| MA0144.1 |  | 1.28e-1 |
| Jaspar motif | Logo | p-value |
|---|
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: CNhs11671
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: CNhs11671
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
UBERON: Anatomy
0000061 (anatomical structure)
0000178 (blood)
0000179 (haemolymphatic fluid)
0000463 (organism substance)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0002193 (hemolymphoid system)
0002390 (hematopoietic system)
0004535 (cardiovascular system)
0007023 (adult organism)
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
