FF:10805-111A4

Name:	anaplastic squamous cell carcinoma cell line:RPMI 2650
Species:	Human (Homo sapiens)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information strain NA tissue nasal septum dev stage NA sex male age unknown cell type unclassifiable cell line RPMI 2650 company JAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank collaboration FANTOM5 OSC CORE (contact: Al Forrest) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type total RNA extraction protocol (Details) OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Download raw sequence, BAM & CTSS
Hg19 BAM CTSS [{{{hg19bam}}} download] [{{{hg19ctss}}} donwload] Hg38 BAM CTSS [{{{hg38bam}}} download] [{{{hg38ctss}}} donwload]

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

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MCL coexpression id	Coexpression_dpi_cluster_scores_median_value
C15-anaplastic-small-skeletal-neuroblastoma-parietal-temporal-tongue	1.038
C180-skeletal-heart-Hepatocyte-acute-occipital-hippocampus-middle	0.527
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma	0.526
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis	0.513
C281-Hodgkin-Reticulocytes-chronic-NK-acute-retinoblastoma-small	0.456
C241-Reticulocytes-chronic-Tracheal-Hodgkin-Endothelial-Hair-thymus	0.434
C147-Neutrophils-Eosinophils-CD4-CD14-CD8-Natural-Peripheral	0.153
C172-chorionic-skeletal-tongue-amniotic-liver-gastrointestinal-Pericytes	0.153
C288-Chondrocyte-Renal-Pericytes-Fibroblast-aorta-Smooth-Meningeal	0.153
C176-Eosinophils-Neutrophils-Mast-CD14-CD4-Basophils-CD19	0.0842

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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

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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: CNhs11889

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MA0131.1		1.02e-1
MA0038.1		1.11e-1
MA0163.1		1.13e-1
MA0048.1		1.19e-1
MA0092.1		1.40e-1
Jaspar motif	Logo	p-value

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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: CNhs11889

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19		1.05e-1
43		1.14e-1
85		1.16e-2
106		1.18e-3
27		1.21e-1
Novel motif	Logo	p-value

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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: CNhs11889

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
DOID:305 carcinoma
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
FF:0104205 RPMI-2650 cell 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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
1749 (squamous cell carcinoma)
305 (carcinoma)
4 (disease)

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