FF:3716-172D2: Difference between revisions
From FANTOM5_SSTAR
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{{f5samples | {{f5samples | ||
| | |ancestors_in_anatomy_facet= | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
| | |comment= | ||
|created_by= | |||
|creation_date= | |||
|def= | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
| Line 66: | Line 33: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|is_a= | |id=FF:3716-172D2 | ||
|is_a=FF:0000103 | |||
|is_obsolete= | |||
|name=macrophage, TB infection, stimulated BMDM+IFNg(caMph), 006hr, biol_rep3 | |||
|namespace= | |namespace= | ||
|part_of= | |part_of= | ||
|profile_cagescan= | |||
|profile_hcage=CNhs11640,LSID804,release016,COMPLETED | |||
|profile_rnaseq= | |||
|profile_srnaseq= | |||
|rna_box=172 | |||
|rna_catalog_number= | |||
|rna_concentration=0.41937 | |||
|rna_extraction_protocol= | |||
|rna_lot_number= | |||
|rna_od260/230=1.93 | |||
|rna_od260/280=2.07 | |||
|rna_position=D2 | |||
|rna_rin=9.1 | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=172D2 | |||
|rna_weight_ug=20.9685 | |||
|sample_age= | |||
|sample_cell_catalog= | |||
|sample_cell_line=UNDEFINED_CELL_LINE | |||
|sample_cell_lot= | |||
|sample_cell_type=macrophage | |||
|sample_collaboration=Frank Brombacher (University of Cape Town, South Africa) | |||
|sample_company= | |||
|sample_description= | |||
|sample_dev_stage=UNDEFINED_DEV_STAGE | |||
|sample_disease= | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity= | |||
|sample_experimental_condition= | |||
|sample_id=3716 | |||
|sample_note= | |||
|sample_sex=male | |||
|sample_species=Mouse (Mus musculus) | |||
|sample_strain=C57BL/6J | |||
|sample_tissue=bone marrow | |||
|top_motifs= | |||
|xref= | |||
}} | }} | ||
Revision as of 03:55, 28 June 2012
| Name: | macrophage, TB infection, stimulated BMDM+IFNg(caMph), 006hr, biol_rep3 |
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| Species: | Mouse (Mus musculus) |
| 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
CNhs11640
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: CNhs11640This 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: CNhs11640This 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: CNhs11640
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
FF:0000103 mouse 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
FF: FANTOM5
NA
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
