Difference between revisions of "FF:10267-104D6"
From FANTOM5_SSTAR
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{{f5samples | {{f5samples | ||
| − | | | + | |ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000211,UBERON:0000465,UBERON:0000468,UBERON:0000479,UBERON:0001062,UBERON:0002384,UBERON:0006659,UBERON:0007023 |
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|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
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|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
| − | | | + | |comment= |
| + | |created_by= | ||
| + | |creation_date= | ||
| + | |def= | ||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
| Line 66: | Line 33: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
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|has_quality= | |has_quality= | ||
| + | |id=FF:10267-104D6 | ||
|is_a=EFO:0002091;;FF:0011152 | |is_a=EFO:0002091;;FF:0011152 | ||
| + | |name= | ||
|namespace= | |namespace= | ||
|part_of= | |part_of= | ||
| + | |profile_cagescan= | ||
| + | |profile_hcage=,,,SKIP_ADDITIONAL | ||
| + | |profile_rnaseq= | ||
| + | |profile_srnaseq= | ||
| + | |rna_box=104 | ||
| + | |rna_catalog_number= | ||
| + | |rna_concentration=0.03978 | ||
| + | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | ||
| + | |rna_lot_number=1-Cl | ||
| + | |rna_od260/230=0.5 | ||
| + | |rna_od260/280=1.99 | ||
| + | |rna_position=D6 | ||
| + | |rna_rin=1.1 | ||
| + | |rna_sample_type=total RNA | ||
| + | |rna_tube_id=104D6 | ||
| + | |rna_weight_ug=1.7901 | ||
| + | |sample_age= | ||
| + | |sample_cell_catalog= | ||
| + | |sample_cell_line= | ||
| + | |sample_cell_lot= | ||
| + | |sample_cell_type=CELL MIXTURE - tissue sample | ||
| + | |sample_collaboration=Alessandro Bonetti | ||
| + | |sample_company= | ||
| + | |sample_description= | ||
| + | |sample_dev_stage= | ||
| + | |sample_disease= | ||
| + | |sample_donor(cell lot)= | ||
| + | |sample_ethnicity= | ||
| + | |sample_experimental_condition= | ||
| + | |sample_id=10267 | ||
| + | |sample_note= | ||
| + | |sample_sex=male | ||
| + | |sample_species=Human (Homo sapiens) | ||
| + | |sample_strain= | ||
| + | |sample_tissue=cruciate ligament | ||
| + | |top_motifs= | ||
}} | }} | ||
Revision as of 05:04, 21 March 2012
| Name: | |
|---|---|
| Species: | Human (Homo sapiens) |
| 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
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
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
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>
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
UBERON: Anatomy
0000061 (anatomical structure)
0000211 (ligament)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
0006659 (cruciate ligament of knee)
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
