FF:11586-120G2: Difference between revisions
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000012,CL:0002321,CL:0000063,CL:0000066,CL:0002371,CL:0000220,CL:0000004,CL:0002202,CL:0000082,CL:0000255,CL:0002076,CL:0002632,CL:0002368,CL:0000322,CL:0000223 | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000012,CL:0002321,CL:0000063,CL:0000066,CL:0002371,CL:0000220,CL:0000004,CL:0002202,CL:0000082,CL:0000255,CL:0002076,CL:0002632,CL:0002368,CL:0000322,CL:0000223 | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|comment= | |comment= | ||
|created_by= | |created_by= | ||
|creation_date= | |creation_date= | ||
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|has_quality= | |has_quality= | ||
|id=FF:11586-120G2 | |id=FF:11586-120G2 | ||
|is_a=EFO:0002091;;FF: | |is_a=EFO:0002091;;FF:0000065 | ||
|is_obsolete= | |||
|name=Fibroblast - Lymphatic, donor2 | |name=Fibroblast - Lymphatic, donor2 | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
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|sample_tissue=lymph node | |sample_tissue=lymph node | ||
|top_motifs= | |top_motifs= | ||
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}} | }} | ||
Revision as of 21:53, 27 June 2012
| Name: | Fibroblast - Lymphatic, donor2 |
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| Species: | Human (Homo sapiens) |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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| Download raw sequence, BAM & CTSS | ||||||||||||
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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: CNhs12082This 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: CNhs12082This 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: CNhs12082
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000065 human fibroblast of lymphatic vessel 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)
0000548 (animal cell)
0002321 (embryonic cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002202 (epithelial cell of tracheobronchial tree)
0000082 (epithelial cell of lung)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002632 (epithelial cell of lower respiratory tract)
0002368 (respiratory epithelial cell)
0000322 (pneumocyte)
0000223 (endodermal cell)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002048 (lung)
0002100 (trunk)
0000483 (epithelium)
0004821 (pulmonary alveolus epithelium)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000480 (anatomical group)
0000923 (germ layer)
0003914 (epithelial tube)
0007499 (epithelial sac)
0002050 (embryonic structure)
0004802 (respiratory tract epithelium)
0005153 (epithelial bud)
0005911 (endo-epithelium)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0006914 (squamous epithelium)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0005178 (thoracic cavity element)
0000487 (simple squamous epithelium)
0000072 (segment of respiratory tract)
0005177 (trunk region element)
0004807 (respiratory system epithelium)
0000117 (respiratory tube)
0000171 (respiration organ)
0003104 (mesenchyme)
0000115 (lung epithelium)
0000464 (anatomical space)
0003215 (alveolus)
0001048 (primordium)
0000925 (endoderm)
0005181 (thoracic segment organ)
0006598 (presumptive structure)
0004185 (endodermal part of digestive tract)
0005157 (epithelial fold)
0009856 (sac)
0002532 (epiblast (generic))
0002299 (alveolus of lung)
0007196 (tracheobronchial tree)
0001555 (digestive tract)
0000065 (respiratory tract)
0001558 (lower respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0007026 (primitive gut)
0001041 (foregut)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)
0006524 (alveolar system)
0008874 (pulmonary acinus)
0002169 (alveolar sac)
0009142 (entire embryonic mesenchyme)
0004894 (alveolar wall)
0008947 (respiratory primordium)
0003258 (endoderm of foregut)
0005597 (lung primordium)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0000118 (lung bud)
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
