FF:11960-126C7: Difference between revisions
From FANTOM5_SSTAR
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|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316 | |ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316 | ||
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|is_a=EFO:0000270;;FF:0000002;;FF:0000210;;UBERON:0004225 | |is_a=EFO:0000270;;FF:0000002;;FF:0000210;;UBERON:0004225 | ||
|is_obsolete= | |is_obsolete= | ||
|library_id_phase_based=2:CNhs14183 | |||
|name=Smooth muscle cells - airway, asthmatic, donor1 | |name=Smooth muscle cells - airway, asthmatic, donor1 | ||
|namespace= | |namespace= | ||
Revision as of 13:57, 18 June 2014
| Name: | Smooth muscle cells - airway, asthmatic, donor1 |
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| Species: | Human (Homo sapiens) |
| Library ID: | {{{library_id}}} |
| Sample type: | primary cells |
| 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: CNhs14183This 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: CNhs14183This 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: CNhs14183
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0000270
FF:0000002 in vivo cell sample
FF:0000210 human sample
UBERON:0004225 respiratory system smooth muscle
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)
0001135 (smooth muscle tissue)
0000479 (tissue)
0004225 (respiratory system smooth muscle)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002385 (muscle tissue)
0010317 (germ layer / neural crest derived structure)
0001015 (musculature)
0001004 (respiratory system)
0002204 (musculoskeletal system)
0000383 (musculature of body)
FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
