FF:10564-108A6: Difference between revisions
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{{f5samples | {{f5samples | ||
|ancestors_in_anatomy_facet= | |||
|ancestors_in_anatomy_facet= | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002371,CL:0000542,CL:0000219,CL:0000945,CL:0000738,CL:0002087,CL:0002242,CL:0000255 | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL: | |ancestors_in_disease_facet=DOID:4,DOID:630,DOID:0050177,DOID:0050427 | ||
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001,FF:0101522 | |||
|comment= | |comment= | ||
|created_by= | |created_by= | ||
|creation_date= | |creation_date= | ||
|def= | |def= | ||
|f5samples= | |||
|ffid_belonging_in_development=CL:0000134,CL:0000051 | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
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|has_quality= | |has_quality= | ||
|id=FF:10564-108A6 | |id=FF:10564-108A6 | ||
|is_a=DOID:0050427 | |is_a=DOID:0050427;;EFO:0002091;;FF:0000210;;FF:0101522 | ||
|is_obsolete= | |||
|name= | |name= | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
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|sample_tissue=blood | |sample_tissue=blood | ||
|top_motifs= | |top_motifs= | ||
|xref= | |||
}} | }} | ||
Latest revision as of 19:22, 9 July 2012
| Name: | |
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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>data
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
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
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>
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
DOID:0050427 xeroderma pigmentosum
EFO:0002091 biological replicate
FF:0000210 human sample
FF:0101522 B-lymphocyte cell line 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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000945 (lymphocyte of B lineage)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
DOID: Disease
4 (disease)
630 (genetic disease)
0050177 (monogenic disease)
0050427 (xeroderma pigmentosum)
FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0101522 (B-lymphocyte cell line 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
CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)
