FF:13423-144D3: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples |id=FF:13423-144D3 |name= |sample_id=13423 |rna_tube_id=144D3 |rna_box=144 |rna_position=D3 |sample_cell_lot= |sample_cell_catalog= |sample_company= |rna_lot_numbe...") |
No edit summary |
||
| Line 1: | Line 1: | ||
{{f5samples | {{f5samples | ||
|id=FF:13423-144D3 | |id=FF:13423-144D3 | ||
|name= | |name=iPS differentiation to neuron, control donor C11-CRL2429, day12, rep1 | ||
|sample_id=13423 | |sample_id=13423 | ||
|rna_tube_id=144D3 | |rna_tube_id=144D3 | ||
| Line 29: | Line 29: | ||
|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=5 | |rna_weight_ug=5.00 | ||
|rna_concentration=0.27 | |rna_concentration=0.27 | ||
|sample_note= | |sample_note= | ||
|profile_hcage= | |profile_hcage=CNhs14047,LSID1158,release016,COMPLETED | ||
|profile_cagescan= | |profile_cagescan= | ||
|profile_srnaseq= | |profile_srnaseq= | ||
| Line 67: | Line 67: | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |top_motifs= | ||
|comment= | |||
|created_by= | |||
|creation_date= | |||
|def= | |||
|has_quality= | |||
|is_a= | |||
|namespace= | |||
|part_of= | |||
}} | }} | ||
Revision as of 13:23, 16 March 2012
| Name: | iPS differentiation to neuron, control donor C11-CRL2429, day12, rep1 |
|---|---|
| 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: CNhs14047This 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: CNhs14047This 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: CNhs14047
FANTOM5 (FF) ontology
Direct parent terms
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
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
