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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000012,CL:0000063,CL:0000066,CL:0002371,CL:0000004,CL:0000255,CL:1000497,CL:0002518,CL:1000507,CL:1000494,CL:1000449
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000012,CL:0000063,CL:0000066,CL:0002371,CL:0000004,CL:0000255,CL:1000497,CL:0002518,CL:1000507,CL:1000494,CL:1000449
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
|comment=Previously: Smooth Muscle Cells - Tracheal, donor2
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|comment=Previously:
 
|created_by=
 
|created_by=
 
|creation_date=
 
|creation_date=
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|has_quality=
 
|has_quality=
 
|id=FF:11593-120G9
 
|id=FF:11593-120G9
|is_a=EFO:0002091;;FF:0000002;;FF:0000151;;FF:0000210
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|is_a=EFO:0002091;;FF:0000184
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|is_obsolete=
 
|name=Smooth Muscle Cells - Tracheal, donor2
 
|name=Smooth Muscle Cells - Tracheal, donor2
 
|namespace=FANTOM5
 
|namespace=FANTOM5
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|sample_tissue=trachea
 
|sample_tissue=trachea
 
|top_motifs=
 
|top_motifs=
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|xref=
 
}}
 
}}

Revision as of 12:56, 27 June 2012


Name:Smooth Muscle Cells - Tracheal, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuetrachea
dev stageNA
sexNA
ageNA
cell typesmooth muscle cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3925
catalog numberSC3415
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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.
Analyst:NA

link to dataset.
data
No results for this sample

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


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

library id: CNhs12567This sample isn't target for the analysis

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

library id: CNhs12567This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs12567


FANTOM5 (FF) ontology


Direct parent terms


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
1000497 (kidney cell)
0002518 (kidney epithelial cell)
1000507 (kidney tubule cell)
1000494 (nephron tubule epithelial cell)
1000449 (epithelial cell of nephron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002113 (kidney)
0002100 (trunk)
0000483 (epithelium)
0000926 (mesoderm)
0000080 (mesonephros)
0000479 (tissue)
0000058 (duct)
0000064 (organ part)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
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)
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)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0004211 (nephron epithelium)
0009773 (renal tubule)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0003104 (mesenchyme)
0005172 (abdomen element)
0000464 (anatomical space)
0009201 (nephric duct)
0005256 (trunk mesenchyme)
0003918 (kidney mesenchyme)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0004819 (kidney epithelium)
0005173 (abdominal segment element)
0001231 (nephron tubule)
0004810 (nephron tubule epithelium)
0002532 (epiblast (generic))
0006553 (renal duct)
0001285 (nephron)
0001008 (renal system)
0003074 (mesonephric duct)
0002417 (abdominal segment of trunk)
0007684 (uriniferous tubule)
0000916 (abdomen)
0003887 (intraembryonic coelom)
0002120 (pronephros)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0003064 (intermediate mesoderm)
0004875 (nephrogenic cord)
0003220 (metanephric mesenchyme)
0006603 (presumptive mesoderm)
0004876 (urogenital ridge)
0004208 (nephrogenic mesenchyme)
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