FF:13295-142H1: Difference between revisions
From FANTOM5_SSTAR
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|id=FF:13295-142H1
|name=trophoblast stem cell line Rybp differentiation, day05, biol_rep1
|sample_id=13295
|rna_tube_id=142H1
|rna_box=142
|rna_position=H1
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|rna_sample_type= | |rna_sample_type= | ||
|rna_extraction_protocol= | |rna_extraction_protocol= | ||
|rna_weight_ug=29. | |rna_weight_ug=29.75 | ||
|rna_concentration=1. | |rna_concentration=1.19 | ||
|sample_note= | |sample_note= | ||
|profile_hcage=CNhs13524,LSID1025,, | |profile_hcage=CNhs13524,LSID1025,release012,COMPLETED | ||
|profile_cagescan=,,, | |profile_cagescan=,,, | ||
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|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0000626 | |fonse_cell_line=FF:0000626 | ||
|fonse_cell_line_closure=FF:0000626 | |fonse_cell_line_closure=FF:0000626 | ||
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|fonse_treatment=EFO:0000369,FF:0000644,FF:0011206,FF:13295-142H1 | |fonse_treatment=EFO:0000369,FF:0000644,FF:0011206,FF:13295-142H1 | ||
|fonse_treatment_closure=EFO:0000369,FF:0000644,FF:0011206,FF:13295-142H1 | |fonse_treatment_closure=EFO:0000369,FF:0000644,FF:0011206,FF:13295-142H1 | ||
|top_motifs= | |||
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Revision as of 17:59, 27 February 2012
| Name: | trophoblast stem cell line Rybp differentiation, day05, biol_rep1 |
|---|---|
| Species: | Mouse (Mus musculus) |
| 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>data
CNhs13524
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: CNhs13524This 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: CNhs13524This 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: CNhs13524
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)
0000034 (stem cell)
0000255 (eukaryotic cell)
0000349 (extraembryonic cell)
0000351 (trophoblast cell)
0000548 (animal cell)
0002371 (somatic cell)
UBERON: Anatomy
0000061 (anatomical structure)
0000358 (blastocyst)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0001062 (anatomical entity)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
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
