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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0001003,UBERON:0002097,UBERON:0002199,UBERON:0001723,UBERON:0000483,UBERON:0002448,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=
|f5samples=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 16:10, 8 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
tissuetongue epidermis (fungiform 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 number3-Te1
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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000922 (embryo)
0001003 (skin epidermis)
0002097 (skin of body)
0002199 (integument)
0001723 (tongue)
0000483 (epithelium)
0002448 (fungiform 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)<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

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