FF:10491-107B5

Name:
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 prostate dev stage NA sex male age 50 cell type unclassifiable cell line LNCap.FGC company RIKEN Bioresource centre collaboration Yukio Nakamura (RIKEN BRC) 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

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

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

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000210 human sample
FF:0104959 C4-2B cell

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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
7 (disease of anatomical entity)
305 (carcinoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002367 (prostate gland)
0002100 (trunk)
0000483 (epithelium)
0002530 (gland)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0005156 (reproductive structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0006554 (urinary system structure)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0000990 (reproductive system)
0002050 (embryonic structure)
0005153 (epithelial bud)
0005911 (endo-epithelium)
0004921 (subdivision of digestive tract)
0000161 (orifice)
0000162 (cloaca)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0005291 (embryonic tissue)
0003102 (surface structure)
0003929 (gut epithelium)
0003104 (mesenchyme)
0010147 (male accessory sex gland)
0005256 (trunk mesenchyme)
0000925 (endoderm)
0006598 (presumptive structure)
0009846 (embryonic cloacal epithelium)
0004185 (endodermal part of digestive tract)
0005157 (epithelial fold)
0003937 (sex gland)
0005399 (male reproductive gland)
0002532 (epiblast (generic))
0003353 (epithelium of hindgut)
0004902 (urogenital sinus epithelium)
0001555 (digestive tract)
0001008 (renal system)
0003101 (male organism)
0004122 (genitourinary system)
0001353 (anal region)
0000163 (embryonic cloaca)
0000079 (male reproductive system)
0007026 (primitive gut)
0006866 (terminal part of digestive tract)
0009142 (entire embryonic mesenchyme)
0001046 (hindgut)
0000164 (primitive urogenital sinus)
0003064 (intermediate mesoderm)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0000931 (proctodeum)
0003820 (prostate bud)
0009847 (prostate field)

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