FF:12865-137E3: Difference between revisions
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{{f5samples | {{f5samples | ||
|DRA_sample_Accession=CAGE@SAMD00021581 | |DRA_sample_Accession=CAGE@SAMD00021581 | ||
|accession_numbers=CAGE;DRX022892;DRR025231;DRZ003656;DRZ004539 | |accession_numbers=CAGE;DRX022892;DRR025231;DRZ003656;DRZ004539;DRZ008397;DRZ009280 | ||
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001474,UBERON:0002384,UBERON:0000479,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0002204,UBERON:0001434 | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001474,UBERON:0002384,UBERON:0000479,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0002204,UBERON:0001434 | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000055,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000062 | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000055,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000062 | ||
| Line 41: | Line 41: | ||
|fonse_treatment_closure=EFO:0000369,FF:0000332,FF:0000600,FF:12865-137E3 | |fonse_treatment_closure=EFO:0000369,FF:0000332,FF:0000600,FF:12865-137E3 | ||
|has_quality= | |has_quality= | ||
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Saos-2%2520osteosarcoma%2520treated%2520with%2520ascorbic%2520acid%2520and%2520BGP%2520to%2520induce%2520calcification%252c%252002hr00min%252c%2520biol_rep3%2520%2528A3%2520T7%2529.CNhs12881.12865-137E3.hg19.nobarcode.bam | |||
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Saos-2%2520osteosarcoma%2520treated%2520with%2520ascorbic%2520acid%2520and%2520BGP%2520to%2520induce%2520calcification%252c%252002hr00min%252c%2520biol_rep3%2520%2528A3%2520T7%2529.CNhs12881.12865-137E3.hg19.ctss.bed.gz | |||
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Saos-2%2520osteosarcoma%2520treated%2520with%2520ascorbic%2520acid%2520and%2520BGP%2520to%2520induce%2520calcification%252c%252002hr00min%252c%2520biol_rep3%2520%2528A3%2520T7%2529.CNhs12881.12865-137E3.hg19.nobarcode.rdna.fa.gz | |||
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Saos-2%2520osteosarcoma%2520treated%2520with%2520ascorbic%2520acid%2520and%2520BGP%2520to%2520induce%2520calcification%252c%252002hr00min%252c%2520biol_rep3%2520%2528A3%2520T7%2529.CNhs12881.12865-137E3.hg38.nobarcode.bam | |||
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Saos-2%2520osteosarcoma%2520treated%2520with%2520ascorbic%2520acid%2520and%2520BGP%2520to%2520induce%2520calcification%252c%252002hr00min%252c%2520biol_rep3%2520%2528A3%2520T7%2529.CNhs12881.12865-137E3.hg38.nobarcode.ctss.bed.gz | |||
|id=FF:12865-137E3 | |id=FF:12865-137E3 | ||
|is_a=EFO:0002091;;FF:0000600 | |is_a=EFO:0002091;;FF:0000600 | ||
| Line 46: | Line 51: | ||
|library_id=CNhs12881 | |library_id=CNhs12881 | ||
|library_id_phase_based=2:CNhs12881 | |library_id_phase_based=2:CNhs12881 | ||
|microRNAs= | |||
|microRNAs_nn= | |||
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;12865 | |||
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;12865 | |||
|name=Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification | |name=Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
| Line 89: | Line 98: | ||
|top_motifs= | |top_motifs= | ||
|xref= | |xref= | ||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:12865-137E3;search_select_hide=table117:FF:12865-137E3 | |||
}} | }} | ||
Latest revision as of 18:46, 4 June 2020
| Name: | Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | CNhs12881 |
| Sample type: | time courses |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| ZENBU report : | 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>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: CNhs12881This 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: CNhs12881This 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: CNhs12881
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000600 human Saos2 osteosarcoma cell line 2h after induction of calcification with ascorbate and BPG 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)
0000055 (non-terminally differentiated cell)
0000003 (native cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000062 (osteoblast)
UBERON: Anatomy
0000468 (multi-cellular organism)
0001474 (bone element)
0002384 (connective tissue)
0000479 (tissue)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0002204 (musculoskeletal system)
0001434 (skeletal system)
FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000350 (experimentally modified sample)
0000359 (2 hr sample)
0000332 (calcification induced with ascorbate and BPG sample)
0100971 (SAOS-2 cell sample)
0100385 (bone cancer cell line sample)
0100407 (osteosarcoma cell line sample)
0000600 (human Saos2 osteosarcoma cell line 2h after induction of calcification with ascorbate and BPG 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:0000335 (mesenchyme condensation cell)
