Difference between revisions of "FF:10634-108I4"
From FANTOM5_SSTAR
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{{f5samples | {{f5samples | ||
| − | + | |ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062 | |
| − | |ancestors_in_anatomy_facet=UBERON: | + | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000057 |
| − | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL: | + | |ancestors_in_disease_facet=DOID:4,DOID:630,DOID:0050177,DOID:1485 |
| − | + | |ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001,FF:0100453 | |
|comment= | |comment= | ||
|created_by= | |created_by= | ||
|creation_date= | |creation_date= | ||
|def= | |def= | ||
| + | |f5samples= | ||
| + | |ffid_belonging_in_development=CL:0000134 | ||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
| Line 37: | Line 39: | ||
|id=FF:10634-108I4 | |id=FF:10634-108I4 | ||
|is_a=DOID:1485;;EFO:0002091;;FF:0000210;;FF:0100453 | |is_a=DOID:1485;;EFO:0002091;;FF:0000210;;FF:0100453 | ||
| + | |is_obsolete= | ||
|name= | |name= | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
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|sample_tissue=skin | |sample_tissue=skin | ||
|top_motifs= | |top_motifs= | ||
| + | |xref= | ||
}} | }} | ||
Latest revision as of 10:31, 9 July 2012
| Name: | |
|---|---|
| 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.
Analyst:NA
link to dataset.
data
Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to
the median expression in the FANTOM5 collection is shown. Value is log10
transformed.
Analyst:NA
link to dataset.
data
no result for this sample
TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample
JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this
sample. Pearson's correlation between the number of TFBSs estimated by
using the position-weight matrix for each promoter and its expression is
expressed as Z-score by taking the ones based on random position-weight
matrix, and the tail probability of the normal distribution corresponding
to the Z-score is taken as the resulting P-value. Lower P-value indicates
more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon
link to dataset.
data
FANTOM5 phase1 novel unique motifsSummary: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 in
169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon
link to dataset.
data
de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
DOID:1485 cystic fibrosis
EFO:0002091 biological replicate
FF:0000210 human sample
FF:0100453 fibroblast cell line sample
Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji
link to source data
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)
UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100453 (fibroblast cell line sample)
Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji
link to source data
data
CL:0000134 (mesenchymal cell)
