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Revision as of 09:58, 27 June 2012


Name:
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebladder
dev stageNA
sexmale
age63
cell typeepithelial cell, transitional
cell lineRT4
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{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


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


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)
1001319 (bladder cell)
1000600 (lower urinary tract cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0060072 (benign neoplasm)
0050687 (cell type cancer)
0060084 (cell type benign neoplasm)
2615 (papilloma)
305 (carcinoma)
2670 (transitional papilloma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0001255 (urinary bladder)
0002100 (trunk)
0000483 (epithelium)
0004645 (urinary bladder urothelium)
0005910 (transitional epithelium)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
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)
0002050 (embryonic structure)
0005911 (endo-epithelium)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000161 (orifice)
0000162 (cloaca)
0005423 (developing anatomical structure)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000119 (cell layer)
0003103 (compound organ)
0005291 (embryonic tissue)
0003102 (surface structure)
0002323 (body cavity)
0000489 (cavitated compound organ)
0003350 (epithelium of mucosa)
0005177 (trunk region element)
0000486 (multilaminar epithelium)
0003104 (mesenchyme)
0000464 (anatomical space)
0004458 (body cavity or lining)
0005256 (trunk mesenchyme)
0000925 (endoderm)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0000365 (urothelium)
0004185 (endodermal part of digestive tract)
0002532 (epiblast (generic))
0001555 (digestive tract)
0001556 (lower urinary tract)
0001008 (renal system)
0004122 (genitourinary system)
0001353 (anal region)
0000163 (embryonic cloaca)
0007026 (primitive gut)
0001256 (wall of urinary bladder)
0006866 (terminal part of digestive tract)
0009142 (entire embryonic mesenchyme)
0001046 (hindgut)
0001259 (mucosa of urinary bladder)
0000164 (primitive urogenital sinus)
0003064 (intermediate mesoderm)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0000931 (proctodeum)

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