FF:10495-107B9: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| Line 36: | Line 36: | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|id= | |id=FF:10495-107B9 | ||
|is_a=DOID:6193;;EFO:0002091;;FF:0000003;;FF:0000210 | |is_a=DOID:6193;;EFO:0002091;;FF:0000003;;FF:0000210 | ||
|is_obsolete= | |is_obsolete= | ||
|name= | |name=epithelioid sarcoma cell line:HS-ES-2R | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan= | |profile_cagescan= | ||
|profile_hcage= | |profile_hcage=CNhs14239,LSID1178,release016,COMPLETED | ||
|profile_rnaseq= | |profile_rnaseq= | ||
|profile_srnaseq= | |profile_srnaseq= | ||
|rna_box= | |rna_box=107 | ||
|rna_catalog_number= | |rna_catalog_number= | ||
|rna_concentration= | |rna_concentration=1.04617 | ||
|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=2.05 | ||
|rna_od260/280= | |rna_od260/280=2.11 | ||
|rna_position= | |rna_position=B9 | ||
|rna_rin= | |rna_rin= | ||
|rna_sample_type= | |rna_sample_type=total RNA | ||
|rna_tube_id= | |rna_tube_id=107B9 | ||
|rna_weight_ug= | |rna_weight_ug=26.15425 | ||
|sample_age= | |sample_age= | ||
|sample_cell_catalog= | |sample_cell_catalog=RCB2361 | ||
|sample_cell_line= | |sample_cell_line=HS-ES-2R | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_type= | |sample_cell_type=unclassifiable | ||
|sample_collaboration= | |sample_collaboration=Yukio Nakamura (RIKEN BRC) | ||
|sample_company= | |sample_company=RIKEN Bioresource centre | ||
|sample_description= | |sample_description= | ||
|sample_dev_stage= | |sample_dev_stage= | ||
|sample_disease= | |sample_disease=epithelioid sarcoma | ||
|sample_donor(cell lot)= | |sample_donor(cell lot)= | ||
|sample_ethnicity= | |sample_ethnicity= | ||
|sample_experimental_condition= | |sample_experimental_condition= | ||
|sample_id= | |sample_id=10495 | ||
|sample_note= | |sample_note= | ||
|sample_sex= | |sample_sex=unknown | ||
|sample_species= | |sample_species=Human (Homo sapiens) | ||
|sample_strain= | |sample_strain= | ||
|sample_tissue= | |sample_tissue=ANATOMICAL SYSTEM | ||
|top_motifs= | |top_motifs= | ||
|xref= | |xref= | ||
}} | }} | ||
Revision as of 15:51, 6 July 2012
| Name: | epithelioid sarcoma cell line:HS-ES-2R |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
| Download raw sequence, BAM & CTSS | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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>dataNo results for this sample
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: CNhs14239This 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: CNhs14239This 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: CNhs14239
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
DOID:6193 epithelioid sarcoma
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human 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
DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
3350 (mesenchymal cell neoplasm)
6193 (epithelioid sarcoma)
FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (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
NA
