FF:1830-49C7: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
{{f5samples | {{f5samples | ||
|id=FF:1830-49C7 | |id=FF:1830-49C7 | ||
|name=mouse fibroblast cell line: CRL-1658 NIH/3T3 | |name=mouse fibroblast cell line: CRL-1658 NIH/3T3 | ||
|sample_id=1830 | |sample_id=1830 | ||
|rna_tube_id= | |rna_tube_id=49C7 | ||
|rna_box=49 | |rna_box=49 | ||
|rna_position=C7 | |rna_position=C7 | ||
| Line 12: | Line 12: | ||
|rna_catalog_number= | |rna_catalog_number= | ||
|sample_species=Mouse (Mus musculus) | |sample_species=Mouse (Mus musculus) | ||
|sample_strain= | |sample_strain=NIH/Swiss | ||
|sample_dev_stage=embryo | |sample_dev_stage=embryo | ||
|sample_tissue=whole body | |sample_tissue=whole body | ||
|sample_donor(cell lot)= | |sample_donor(cell lot)= | ||
|sample_sex= | |sample_sex=unknown_sex_type | ||
|sample_age= | |sample_age= | ||
|sample_ethnicity= | |sample_ethnicity= | ||
| Line 22: | Line 22: | ||
|rna_od260/230= | |rna_od260/230= | ||
|rna_od260/280= | |rna_od260/280= | ||
|sample_cell_type= | |sample_cell_type=CELL MIXTURE - tissue sample | ||
|sample_cell_line= | |sample_cell_line= | ||
|sample_collaboration= | |sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | ||
|sample_experimental_condition= | |sample_experimental_condition= | ||
|sample_disease= | |sample_disease= | ||
|rna_sample_type= | |rna_sample_type= | ||
|rna_extraction_protocol= | |rna_extraction_protocol= | ||
|rna_weight_ug= | |rna_weight_ug= | ||
Revision as of 17:48, 27 February 2012
| Name: | mouse fibroblast cell line: CRL-1658 NIH/3T3 |
|---|---|
| Species: | Mouse (Mus musculus) |
| 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
CNhs11093
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: CNhs11093
| MA0100.1 |  | 1.01e-2 |
| MA0140.1 |  | 1.01e-3 |
| MA0101.1 |  | 1.02e-1 |
| MA0017.1 |  | 1.04e-2 |
| MA0039.2 |  | 1.10e-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: CNhs11093
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: CNhs11093
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)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0001062 (anatomical entity)
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
