FF:11671-122G6

Name:	Alveolar Epithelial Cells, donor3
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 lung dev stage NA sex NA age NA cell type epithelial cell of lung, small airway cell line NA company Sciencell/3H collaboration FANTOM5 OSC CORE (contact: Al Forrest) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number SC3205 sample type total RNA extraction protocol (Details) OP-RNA-extraction-totalRNA-TRIzol-ethanol-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. <br>Analyst:NA <br><br>link to dataset.<br>dataNo results for this sample

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
library id: CNhs12119This sample isn't target for the analysis

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
library id: CNhs12119This sample isn't target for the analysis

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> library id: CNhs12119

FANTOM5 (FF) ontology

---

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000002 in vivo cell sample
FF:0000012 human alveolar epithelial cell sample
FF:0000210 human sample

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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000082 (epithelial cell of lung)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000322 (pneumocyte)
0000548 (animal cell)
0002076 (endo-epithelial cell)
0002202 (epithelial cell of tracheobronchial tree)
0002321 (embryonic cell)
0002368 (respiratory epithelial cell)
0002371 (somatic cell)
0002632 (epithelial cell of lower respiratory tract)

UBERON: Anatomy
0000025 (tube)
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000115 (lung epithelium)
0000117 (respiratory tube)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000487 (simple squamous epithelium)
0000490 (unilaminar epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001558 (lower respiratory tract)
0002048 (lung)
0002050 (embryonic structure)
0002169 (alveolar sac)
0002224 (thoracic cavity)
0002299 (alveolus of lung)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003215 (alveolus)
0003258 (endoderm of foregut)
0003914 (epithelial tube)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004802 (respiratory tract epithelium)
0004807 (respiratory system epithelium)
0004821 (pulmonary alveolus epithelium)
0004894 (alveolar wall)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0006524 (alveolar system)
0006914 (squamous epithelium)
0007026 (primitive gut)
0007196 (tracheobronchial tree)
0007499 (epithelial sac)
0008874 (pulmonary acinus)
0008947 (respiratory primordium)
0009142 (entire embryonic mesenchyme)

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