FF:14310-155C8: Difference between revisions
From FANTOM5_SSTAR
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|is_a=EFO:0002091;;FF:0000640 | |is_a=EFO:0002091;;FF:0000640 | ||
|is_obsolete= | |is_obsolete= | ||
|name= | |name=Fibroblast - Aortic Adventitial donor3 (cytoplasmic fraction) | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan= | |profile_cagescan= | ||
|profile_hcage=,,, | |profile_hcage=CNhs14559,LSID1334,,COMPLETED | ||
|profile_rnaseq= | |profile_rnaseq= | ||
|profile_srnaseq= | |profile_srnaseq= | ||
|rna_box=155 | |rna_box=155 | ||
|rna_catalog_number= | |rna_catalog_number= | ||
|rna_concentration=1.13176 | |rna_concentration=1.13176 | ||
|rna_extraction_protocol= | |rna_extraction_protocol= | ||
|rna_lot_number= | |rna_lot_number= | ||
|rna_od260/230= | |rna_od260/230= | ||
|rna_od260/280= | |rna_od260/280= | ||
|rna_position=C8 | |rna_position=C8 | ||
|rna_rin= | |rna_rin= | ||
| Line 57: | Line 57: | ||
|rna_tube_id=155C8 | |rna_tube_id=155C8 | ||
|rna_weight_ug=84.882 | |rna_weight_ug=84.882 | ||
|sample_age= | |sample_age= | ||
|sample_cell_catalog= | |sample_cell_catalog= | ||
|sample_cell_line= | |sample_cell_line=UNDEFINED_CELL_LINE | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_type=fibroblast | |sample_cell_type=fibroblast | ||
|sample_collaboration= | |sample_collaboration=UNDEFINED_COLLABORATION | ||
|sample_company= | |sample_company= | ||
|sample_description= | |sample_description= | ||
|sample_dev_stage=19 years old adult | |sample_dev_stage=19 years old adult | ||
|sample_disease= | |sample_disease= | ||
|sample_donor(cell lot)= | |sample_donor(cell lot)= | ||
|sample_ethnicity= | |sample_ethnicity= | ||
|sample_experimental_condition= | |sample_experimental_condition=UNDEFINED_CONDITION | ||
|sample_id=14310 | |sample_id=14310 | ||
|sample_note= | |sample_note= | ||
|sample_sex=female | |sample_sex=female | ||
|sample_species=Human (Homo sapiens) | |sample_species=Human (Homo sapiens) | ||
|sample_strain= | |sample_strain=UNDEFINED_STRAIN | ||
|sample_tissue=aorta | |sample_tissue=aorta | ||
|top_motifs= | |top_motifs= | ||
|xref= | |xref= | ||
}} | }} | ||
Revision as of 17:34, 6 July 2012
| Name: | Fibroblast - Aortic Adventitial donor3 (cytoplasmic fraction) |
|---|---|
| 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: CNhs14559This 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: CNhs14559This 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: CNhs14559
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000640 human Fibroblast - Aortic Adventitial, cytoplasmic fraction 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)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000057 (fibroblast)
1000306 (fibroblast of tunica adventitia of artery)
0002547 (fibroblast of the aortic adventitia)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000947 (aorta)
0001637 (artery)
0000483 (epithelium)
0002384 (connective tissue)
0000479 (tissue)
0000055 (vessel)
0000064 (organ part)
0000062 (organ)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0004923 (organ component layer)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0004573 (systemic artery)
0003509 (arterial blood vessel)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0002049 (vasculature)
0004797 (blood vessel layer)
0010317 (germ layer / neural crest derived structure)
0007798 (vascular system)
0000415 (artery wall)
0007240 (tunica adventitia of artery)
0005742 (adventitia)
0005734 (tunica adventitia of blood vessel)
0004664 (aorta tunica adventitia)
0004535 (cardiovascular system)
0004571 (systemic arterial system)
0010191 (aortic system)
0004572 (arterial system)
0004537 (blood vasculature)
0001009 (circulatory system)
0004663 (aorta wall)
FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000057 (fibroblast sample)
0000001 (sample)
0000408 (cellular fractionation sample)
0000350 (experimentally modified sample)
0000058 (human fibroblast of the aortic adventitia sample)
0000405 (cytoplasmic fraction sample)
0000640 (human Fibroblast - Aortic Adventitial, cytoplasmic fraction 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
NA
