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{{f5samples
 
{{f5samples
|F5samples=
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|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0001003,UBERON:0002097,UBERON:0002199,UBERON:0001723,UBERON:0000483,UBERON:0000396,UBERON:0006562,UBERON:0000033,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0000077,UBERON:0004121,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004921,UBERON:0000161,UBERON:0005423,UBERON:0001444,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001726,UBERON:0001062,UBERON:0000119,UBERON:0003103,UBERON:0005291,UBERON:0003102,UBERON:0000020,UBERON:0007376,UBERON:0000078,UBERON:0000072,UBERON:0003104,UBERON:0001032,UBERON:0000925,UBERON:0006598,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0000065,UBERON:0001004,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0000165,UBERON:0007026,UBERON:0001041,UBERON:0004456,UBERON:0000166,UBERON:0001557,UBERON:0001033,UBERON:0009471,UBERON:0001042,UBERON:0002416,UBERON:0008814,UBERON:0009142,UBERON:0000930,UBERON:0006601,UBERON:0006595,UBERON:0006603,UBERON:0007383,UBERON:0009145,UBERON:0010056
|ancestors_in_anatomy_facet=UBERON:0000005,UBERON:0000020,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000073,UBERON:0000119,UBERON:0000153,UBERON:0000165,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000925,UBERON:0000930,UBERON:0001003,UBERON:0001007,UBERON:0001016,UBERON:0001032,UBERON:0001033,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0001723,UBERON:0001726,UBERON:0002050,UBERON:0002097,UBERON:0002199,UBERON:0002416,UBERON:0002532,UBERON:0002539,UBERON:0003102,UBERON:0003212,UBERON:0004119,UBERON:0004121,UBERON:0004362,UBERON:0004456,UBERON:0005423,UBERON:0005726,UBERON:0006260,UBERON:0006756,UBERON:0006757,UBERON:0007023,UBERON:0007026,UBERON:0007376,UBERON:0007383,UBERON:0008814,UBERON:0008816,UBERON:0009471
 
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
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|creation_date=
 
|creation_date=
 
|def=
 
|def=
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|f5samples=
 
|fonse_cell_line=
 
|fonse_cell_line=
 
|fonse_cell_line_closure=
 
|fonse_cell_line_closure=

Revision as of 07:08, 8 June 2012


Name:tongue epidermis (vallate papillae), donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuetongue epidermis (vallate papillae)
dev stageNA
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationAlessandro Bonetti
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1-Te2
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.
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


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


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000922 (embryo)
0001003 (skin epidermis)
0002097 (skin of body)
0002199 (integument)
0001723 (tongue)
0000483 (epithelium)
0000396 (vallate papilla)
0006562 (pharynx)
0000033 (head)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0004921 (subdivision of digestive tract)
0000161 (orifice)
0005423 (developing anatomical structure)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001726 (papilla of tongue)
0001062 (anatomical entity)
0000119 (cell layer)
0003103 (compound organ)
0005291 (embryonic tissue)
0003102 (surface structure)
0000020 (sense organ)
0007376 (outer epithelium)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000072 (segment of respiratory tract)
0003104 (mesenchyme)
0001032 (sensory system)
0000925 (endoderm)
0006598 (presumptive structure)
0004185 (endodermal part of digestive tract)
0002532 (epiblast (generic))
0001555 (digestive tract)
0000065 (respiratory tract)
0001004 (respiratory system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000924 (ectoderm)
0000165 (mouth)
0007026 (primitive gut)
0001041 (foregut)
0004456 (entire sense organ system)
0000166 (oral opening)
0001557 (upper respiratory tract)
0001033 (gustatory system)
0009471 (dorsum of tongue)
0001042 (chordate pharynx)
0002416 (integumental system)
0008814 (pharyngeal arch system)
0009142 (entire embryonic mesenchyme)
0000930 (stomodeum)
0006601 (presumptive ectoderm)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0007383 (enveloping layer of ectoderm)
0009145 (pharyngeal region of foregut)
0010056 (future tongue)

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