FF:10626-108H5: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |F5samples= | ||
| | |ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet=DOID:0050687,DOID:1115,DOID:14566,DOID:162,DOID:4 | |ancestors_in_disease_facet=DOID:0050687,DOID:1115,DOID:14566,DOID:162,DOID:4 | ||
| | |comment= | ||
|created_by= | |||
|creation_date= | |||
|def= | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
| Line 66: | Line 34: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|id=FF:10626-108H5 | |||
|is_a=EFO:0002091;;FF:0000210;;FF:0102267 | |is_a=EFO:0002091;;FF:0000210;;FF:0102267 | ||
|name= | |||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan= | |||
|profile_hcage=,,,IN_LIBRARIAN | |||
|profile_rnaseq= | |||
|profile_srnaseq= | |||
|rna_box=108 | |||
|rna_catalog_number= | |||
|rna_concentration=0.85793 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number= | |||
|rna_od260/230=1.91 | |||
|rna_od260/280=2.12 | |||
|rna_position=H5 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=108H5 | |||
|rna_weight_ug=40.32271 | |||
|sample_age=7 | |||
|sample_cell_catalog=RCB1188 | |||
|sample_cell_line=NRS-1 | |||
|sample_cell_lot= | |||
|sample_cell_type=skeletal muscle cell | |||
|sample_collaboration=Yukio Nakamura (RIKEN BRC) | |||
|sample_company=RIKEN Bioresource centre | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease=rhabdomyosarcoma | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity=unknown | |||
|sample_experimental_condition= | |||
|sample_id=10626 | |||
|sample_note= | |||
|sample_sex=female | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=skeletal muscle | |||
|top_motifs= | |||
}} | }} | ||
Revision as of 14:11, 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
is_a relathionship
EFO:0002091 biological replicate
FF:0000210 human sample
FF:0102267 rhabdomyosarcoma cell line 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
DOID: Disease
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)
UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
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
