FF:10713-109I2: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |F5samples= | ||
| | |ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0001062,UBERON:0002097,UBERON:0002199,UBERON:0002416,UBERON:0003102 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet=DOID:0050686,DOID:0060122,DOID:14566,DOID:162,DOID:3149,DOID:3151,DOID:3451,DOID:4,DOID:4159 | |ancestors_in_disease_facet=DOID:0050686,DOID:0060122,DOID:14566,DOID:162,DOID:3149,DOID:3151,DOID:3451,DOID:4,DOID:4159 | ||
| | |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:10713-109I2 | |||
|is_a=DOID:3149;;EFO:0002091;;FF:0000003;;FF:0000210;;UBERON:0000014 | |is_a=DOID:3149;;EFO:0002091;;FF:0000003;;FF:0000210;;UBERON:0000014 | ||
|name= | |||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan= | |||
|profile_hcage=,,,IN_LIBRARIAN | |||
|profile_rnaseq= | |||
|profile_srnaseq= | |||
|rna_box=109 | |||
|rna_catalog_number= | |||
|rna_concentration=0.45006 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number= | |||
|rna_od260/230=1.92 | |||
|rna_od260/280=2 | |||
|rna_position=I2 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=109I2 | |||
|rna_weight_ug=21.15282 | |||
|sample_age=57 | |||
|sample_cell_catalog=CRL-7630 | |||
|sample_cell_line=Hs 892.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=keratoacanthoma | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity=C | |||
|sample_experimental_condition= | |||
|sample_id=10713 | |||
|sample_note= | |||
|sample_sex=female | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=skin | |||
|top_motifs= | |||
}} | }} | ||
Revision as of 14:13, 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
DOID:3149 keratoacanthoma
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
UBERON:0000014 zone of skin
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
0050686 (organ system cancer)
0060122 (integumentary system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
3149 (keratoacanthoma)
3151 (skin squamous cell carcinoma)
3451 (skin carcinoma)
4 (disease)
4159 (skin cancer)
UBERON: Anatomy
0000014 (zone of skin)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0001062 (anatomical entity)
0002097 (skin of body)
0002199 (integument)
0002416 (integumental system)
0003102 (surface structure)
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
