FF:10346-105D4

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 Ureter dev stage NA sex male age NA cell type CELL MIXTURE - tissue sample cell line NA company NA collaboration Alessandro Bonetti External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number 3-Ur 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.
Analyst:NA

link to dataset.
data

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
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 motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011180 Ureter

Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000922 (embryo)
0002113 (kidney)
0002100 (trunk)
0000056 (ureter)
0000483 (epithelium)
0000926 (mesoderm)
0000080 (mesonephros)
0000479 (tissue)
0000058 (duct)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
0005179 (pelvis organ)
0006555 (excretory tube)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0003914 (epithelial tube)
0005103 (mesonephric epithelium)
0000083 (mesonephric tubule)
0007499 (epithelial sac)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0000489 (cavitated compound organ)
0000485 (simple columnar epithelium)
0005177 (trunk region element)
0003104 (mesenchyme)
0005172 (abdomen element)
0000464 (anatomical space)
0007497 (developing epithelial placode)
0009201 (nephric duct)
0005256 (trunk mesenchyme)
0001048 (primordium)
0003918 (kidney mesenchyme)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0004819 (kidney epithelium)
0000084 (ureteric bud)
0005173 (abdominal segment element)
0009856 (sac)
0002532 (epiblast (generic))
0006553 (renal duct)
0001008 (renal system)
0002355 (pelvis)
0003074 (mesonephric duct)
0002417 (abdominal segment of trunk)
0000916 (abdomen)
0003887 (intraembryonic coelom)
0002120 (pronephros)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0003064 (intermediate mesoderm)
0004875 (nephrogenic cord)
0005081 (ureter ureteric bud)
0006603 (presumptive mesoderm)
0004876 (urogenital ridge)
0005095 (kidney rudiment)
0005721 (pronephric mesoderm)
0005754 (rostral part of nephrogenic cord)
0003060 (pronephric duct)
0007687 (kidney field)
0007297 (presumptive pronephric mesoderm)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data
NA