FF:13001-139B4: Difference between revisions
From FANTOM5_SSTAR
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|datafreeze_phase=2 | |datafreeze_phase=2 | ||
|def= | |def= | ||
|donor= biol_rep2 | |||
|ffid_belonging_in_development=CL:0000134 | |ffid_belonging_in_development=CL:0000134 | ||
|fonse_cell_line= | |fonse_cell_line= | ||
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|library_id=CNhs12992 | |library_id=CNhs12992 | ||
|library_id_phase_based=2:CNhs12992 | |library_id_phase_based=2:CNhs12992 | ||
|name=EBF KO HPCs induced to T cell | |name=EBF KO HPCs induced to T cell | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
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|sample_strain= | |sample_strain= | ||
|sample_tissue= | |sample_tissue= | ||
|time= day05 | |||
|timecourse=mouse_T_cell | |timecourse=mouse_T_cell | ||
|top_motifs= | |top_motifs= | ||
|xref= | |xref= | ||
}} | }} | ||
Revision as of 15:47, 9 January 2015
| Name: | EBF KO HPCs induced to T cell |
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| Species: | Mouse (Mus musculus) |
| Library ID: | CNhs12992 |
| Sample type: | time courses |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
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Sample information
RNA information
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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
CNhs12992
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: CNhs12992This 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: CNhs12992This 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: CNhs12992
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000623 mouse EBF KO HPCs induced to T cell 120h sample
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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000837 (hematopoietic multipotent progenitor cell)
FF: FANTOM5
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000378 (120 hr sample)
0000342 (T-cell induction sample)
0000623 (mouse EBF KO HPCs induced to T cell 120h sample)
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
CL:0000134 (mesenchymal cell)
