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|creation_date=
|creation_date=
|data_phase=2
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|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:CNhs14189
|library_id=
|name=Smooth muscle cells - airway, asthmatic, donor6
|library_id_phase_based=2:
|name="Smooth muscle cells - airway, asthmatic, donor6"
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=
|profile_cagescan=
|profile_hcage=CNhs14189,LSID1177,release016,COMPLETED
|profile_hcage="CNhs14189,LSID1177,release016,COMPLETED"
|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=
|profile_srnaseq=

Revision as of 19:34, 27 November 2014


Name:"Smooth muscle cells - airway, asthmatic, donor6"
Species:Human (Homo sapiens)
Library ID:
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA
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>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: "CNhs14189This 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: "CNhs14189This 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: "CNhs14189


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)

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)