FF:10838-111E1

Name:	medulloblastoma cell line:D283 Med
Species:	Human (Homo sapiens)
Library ID:	CNhs12805
Sample type:	cell lines
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information strain NA tissue brain dev stage NA sex male age 6 cell type neurectodermal cell cell line D283 Med company ATCC 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

CAGE Accession numbers
Method Sample accession id CAGE  SAMD00004791 Library accession numbers Library id Method Exp. accession id Run accession id CNhs12805 CAGE DRX007928 DRR008800 Accession ID Hg19 Library id BAM CTSS CNhs12805 DRZ000225 DRZ001610 Accession ID Hg38 Library id BAM CTSS CNhs12805

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

Relative expression to median (log10)

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Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.

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>dataNo results for this sample

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

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: "CNhs12805This sample isn't target for the analysis

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: "CNhs12805This sample isn't target for the analysis

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: "CNhs12805

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000210 human sample
FF:0101359 medulloblastoma 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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000125 (glial cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
3093 (nervous system cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100711 (glioma cell line sample)
0100255 (brain cell line sample)
0100690 (brain cancer cell line sample)
0101531 (glial cell line sample)
0101359 (medulloblastoma cell line 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
CL:0000133 (neurectodermal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006238 (future brain)
UBERON:0010316 (germ layer / neural crest)