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|name=olfactory epithelium, donor1
|name=olfactory epithelium, donor1
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|sample_tissue=olfactory epithelium
|sample_tissue=olfactory epithelium

Revision as of 08:02, 27 June 2012

Name:olfactory epithelium, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
Additional information
Sample information
tissueolfactory epithelium
dev stageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
collaborationAlessandro Bonetti
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1-Oe
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
[{{{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.

link to dataset.

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.

link to dataset.
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.

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.

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

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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000922 (embryo)
0001997 (olfactory epithelium)
0000483 (epithelium)
0000033 (head)
0000479 (tissue)
0002346 (neurectoderm)
0000344 (mucosa)
0002268 (olfactory organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000466 (immaterial anatomical entity)
0004121 (ectoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0004802 (respiratory tract epithelium)
0005911 (endo-epithelium)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0001444 (subdivision of head)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0005291 (embryonic tissue)
0000020 (sense organ)
0000485 (simple columnar epithelium)
0003350 (epithelium of mucosa)
0000072 (segment of respiratory tract)
0000488 (atypical epithelium)
0004785 (respiratory system mucosa)
0004807 (respiratory system epithelium)
0005384 (nasal cavity epithelium)
0006934 (sensory epithelium)
0001032 (sensory system)
0000464 (anatomical space)
0005085 (ectodermal placode)
0007497 (developing epithelial placode)
0009955 (neurogenic placode)
0002546 (cranial placode)
0001048 (primordium)
0000925 (endoderm)
0006598 (presumptive structure)
0004814 (upper respiratory tract epithelium)
0002532 (epiblast (generic))
0000065 (respiratory tract)
0000010 (peripheral nervous system)
0001004 (respiratory system)
0004089 (midface)
0001016 (nervous system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000924 (ectoderm)
0004456 (entire sense organ system)
0001456 (face)
0000004 (olfactory apparatus)
0001557 (upper respiratory tract)
0001707 (nasal cavity)
0001826 (nasal cavity mucosa)
0000076 (external ectoderm)
0003050 (olfactory placode)
0006601 (presumptive ectoderm)
0006595 (presumptive endoderm)
0005870 (olfactory pit)


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

link to source data