FF:14298-155B5: Difference between revisions
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|is_a=EFO:0002091;;FF:0000210;;FF:0000661 | |is_a=EFO:0002091;;FF:0000210;;FF:0000661 | ||
|is_obsolete= | |is_obsolete= | ||
|name= | |name= | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan= | |profile_cagescan= | ||
|profile_hcage= | |profile_hcage=,,,IN_LIBRARIAN | ||
|profile_rnaseq= | |profile_rnaseq= | ||
|profile_srnaseq= | |profile_srnaseq= | ||
| Line 49: | Line 49: | ||
|rna_catalog_number= | |rna_catalog_number= | ||
|rna_concentration=1.89426 | |rna_concentration=1.89426 | ||
|rna_extraction_protocol= | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | ||
|rna_lot_number= | |rna_lot_number= | ||
|rna_od260/230= | |rna_od260/230=2.07 | ||
|rna_od260/280= | |rna_od260/280=2.08 | ||
|rna_position=B5 | |rna_position=B5 | ||
|rna_rin= | |rna_rin= | ||
|rna_sample_type=total RNA | |rna_sample_type=total RNA | ||
|rna_tube_id=155B5 | |rna_tube_id=155B5 | ||
|rna_weight_ug= | |rna_weight_ug=94.713 | ||
|sample_age= | |sample_age=1 | ||
|sample_cell_catalog= | |sample_cell_catalog= | ||
|sample_cell_line=THP-1 | |sample_cell_line=THP-1 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_type=monoblast | |sample_cell_type=monoblast | ||
|sample_collaboration= | |sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | ||
|sample_company= | |sample_company= | ||
|sample_description= | |sample_description= | ||
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|sample_disease=acute myeloid leukemia (FAB M5) | |sample_disease=acute myeloid leukemia (FAB M5) | ||
|sample_donor(cell lot)= | |sample_donor(cell lot)= | ||
|sample_ethnicity= | |sample_ethnicity=J | ||
|sample_experimental_condition= | |sample_experimental_condition=cytoplasmic RNA | ||
|sample_id=14298 | |sample_id=14298 | ||
|sample_note= | |sample_note= | ||
|sample_sex=male | |sample_sex=male | ||
|sample_species=Human (Homo sapiens) | |sample_species=Human (Homo sapiens) | ||
|sample_strain= | |sample_strain= | ||
|sample_tissue=blood | |sample_tissue=blood | ||
|top_motifs= | |top_motifs= | ||
|xref= | |xref= | ||
}} | }} | ||
Revision as of 12:58, 21 December 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. <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
EFO:0002091 biological replicate
FF:0000210 human sample
FF:0000661 acute myeloid leukemia (FAB M5) cell line:THP-1 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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000766 (myeloid leukocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0000255 (eukaryotic cell)
0000576 (monocyte)
DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
2531 (hematologic cancer)
14566 (disease of cellular proliferation)
0060083 (immune system cancer)
1240 (leukemia)
8692 (myeloid leukemia)
FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100737 (leukemia cell line sample)
0000408 (cellular fractionation sample)
0000350 (experimentally modified sample)
0000405 (cytoplasmic fraction sample)
0101370 (THP-1 cell sample)
0101035 (hematopoietic cell line sample)
0102332 (monocytic leukemia cell line sample)
0100740 (myeloid leukemia cell line sample)
0000661 (acute myeloid leukemia (FAB M5) cell line:THP-1 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
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)
