FF:10738-110B9: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |ancestors_in_anatomy_facet= | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet=DOID:4,DOID:14566,DOID:0060072,DOID:0060084,DOID:2615,DOID:139 | |||
|ancestors_in_disease_facet=DOID: | |ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001 | ||
| | |comment= | ||
|created_by= | |||
|creation_date= | |||
|def= | |||
|f5samples= | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
| Line 66: | Line 35: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |||
|id=FF:10738-110B9 | |||
|is_a=DOID:139;;EFO:0002091;;FF:0000003;;FF:0000210 | |||
|is_obsolete= | |||
|name= | |||
|namespace=FANTOM5 | |||
|part_of= | |||
|profile_cagescan= | |||
|profile_hcage=,,,IN_LIBRARIAN | |||
|profile_rnaseq= | |||
|profile_srnaseq= | |||
|rna_box=110 | |||
|rna_catalog_number= | |||
|rna_concentration=0.5101 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number= | |||
|rna_od260/230=1.86 | |||
|rna_od260/280=2.12 | |||
|rna_position=B9 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=110B9 | |||
|rna_weight_ug=13.7727 | |||
|sample_age=72 | |||
|sample_cell_catalog=CRL-7289 | |||
|sample_cell_line=Hs 416.T | |||
|sample_cell_lot= | |||
|sample_cell_type=unclassifiable | |||
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | |||
|sample_company=ATCC | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease=squamous papilloma | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity=C | |||
|sample_experimental_condition= | |||
|sample_id=10738 | |||
|sample_note= | |||
|sample_sex=male | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=skin | |||
|top_motifs= | |top_motifs= | ||
|xref= | |||
}} | }} | ||
Latest revision as of 19:27, 4 July 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
DOID:139 squamous cell papilloma
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human 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
4 (disease)
14566 (disease of cellular proliferation)
0060072 (benign neoplasm)
0060084 (cell type benign neoplasm)
2615 (papilloma)
139 (squamous cell papilloma)
FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (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
NA
