Difference between revisions of "FF:10749-110D2"
From FANTOM5_SSTAR
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{{f5samples | {{f5samples | ||
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548 | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548 | ||
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|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:2994,DOID:305,DOID:3095,DOID:4 | |ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:2994,DOID:305,DOID:3095,DOID:4 | ||
| − | | | + | |comment= |
| + | |created_by= | ||
| + | |creation_date= | ||
| + | |def= | ||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
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|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
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|has_quality= | |has_quality= | ||
| + | |id=FF:10749-110D2 | ||
|is_a=EFO:0002091;;FF:0000210;;FF:0100946 | |is_a=EFO:0002091;;FF:0000210;;FF:0100946 | ||
| + | |name= | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
| + | |profile_cagescan= | ||
| + | |profile_hcage=,,,IN_LIBRARIAN | ||
| + | |profile_rnaseq= | ||
| + | |profile_srnaseq= | ||
| + | |rna_box=110 | ||
| + | |rna_catalog_number= | ||
| + | |rna_concentration=1.16049 | ||
| + | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | ||
| + | |rna_lot_number= | ||
| + | |rna_od260/230=1.85 | ||
| + | |rna_od260/280=2.09 | ||
| + | |rna_position=D2 | ||
| + | |rna_rin= | ||
| + | |rna_sample_type=total RNA | ||
| + | |rna_tube_id=110D2 | ||
| + | |rna_weight_ug=31.33323 | ||
| + | |sample_age=22 | ||
| + | |sample_cell_catalog=CRL-1973 | ||
| + | |sample_cell_line=NTERA-2 cl.D1 | ||
| + | |sample_cell_lot= | ||
| + | |sample_cell_type=unclassifiable | ||
| + | |sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | ||
| + | |sample_company=ATCC | ||
| + | |sample_description= | ||
| + | |sample_dev_stage= | ||
| + | |sample_disease=teratocarcinoma | ||
| + | |sample_donor(cell lot)= | ||
| + | |sample_ethnicity=C | ||
| + | |sample_experimental_condition= | ||
| + | |sample_id=10749 | ||
| + | |sample_note= | ||
| + | |sample_sex=male | ||
| + | |sample_species=Human (Homo sapiens) | ||
| + | |sample_strain= | ||
| + | |sample_tissue=testis | ||
| + | |top_motifs= | ||
}} | }} | ||
Revision as of 05:14, 21 March 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
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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2994 (germ cell cancer)
305 (carcinoma)
3095 (germ cell and embryonal cancer)
4 (disease)
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
