FF:13651-147B6: Difference between revisions
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{{f5samples | {{f5samples | ||
|accession_numbers=CAGE;DRX023539;DRR025934;DRZ004359;DRZ005186 | |DRA_sample_Accession=CAGE@SAMD00022263 | ||
|accession_numbers=CAGE;DRX023539;DRR025934;DRZ004359;DRZ005186;DRZ009100;DRZ009927 | |||
|ancestors_in_anatomy_facet= | |ancestors_in_anatomy_facet= | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
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|data_phase=2 | |data_phase=2 | ||
|datafreeze_phase=2 | |datafreeze_phase=2 | ||
|donor= biol_rep3 | |||
|has_quality= | |has_quality= | ||
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/ARPE-19%2520EMT%2520induced%2520with%2520TGF-beta%2520and%2520TNF-alpha%252c%252002hr30min%252c%2520biol_rep3.CNhs14490.13651-147B6.hg19.nobarcode.bam | |||
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/ARPE-19%2520EMT%2520induced%2520with%2520TGF-beta%2520and%2520TNF-alpha%252c%252002hr30min%252c%2520biol_rep3.CNhs14490.13651-147B6.hg19.ctss.bed.gz | |||
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/ARPE-19%2520EMT%2520induced%2520with%2520TGF-beta%2520and%2520TNF-alpha%252c%252002hr30min%252c%2520biol_rep3.CNhs14490.13651-147B6.hg19.nobarcode.rdna.fa.gz | |||
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/ARPE-19%2520EMT%2520induced%2520with%2520TGF-beta%2520and%2520TNF-alpha%252c%252002hr30min%252c%2520biol_rep3.CNhs14490.13651-147B6.hg38.nobarcode.bam | |||
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/ARPE-19%2520EMT%2520induced%2520with%2520TGF-beta%2520and%2520TNF-alpha%252c%252002hr30min%252c%2520biol_rep3.CNhs14490.13651-147B6.hg38.nobarcode.ctss.bed.gz | |||
|id=FF:13651-147B6 | |id=FF:13651-147B6 | ||
|is_a= | |is_a= | ||
|library_id=CNhs14490 | |library_id=CNhs14490 | ||
|library_id_phase_based=2:CNhs14490 | |library_id_phase_based=2:CNhs14490 | ||
|name=ARPE-19 EMT induced with TGF-beta and TNF-alpha | |microRNAs= | ||
|microRNAs_nn= | |||
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;13651 | |||
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;13651 | |||
|name=ARPE-19 EMT induced with TGF-beta and TNF-alpha | |||
|part_of= | |part_of= | ||
|profile_cagescan= | |profile_cagescan= | ||
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|sample_strain=UNDEFINED_STRAIN | |sample_strain=UNDEFINED_STRAIN | ||
|sample_tissue=UNDEFINED_TISSUE_TYPE | |sample_tissue=UNDEFINED_TISSUE_TYPE | ||
|timecourse= | |time= 02hr30min | ||
|timecourse=Epithelial_to_mesenchymal | |||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:13651-147B6;search_select_hide=table117:FF:13651-147B6 | |||
}} | }} |
Latest revision as of 19:04, 4 June 2020
Name: | ARPE-19 EMT induced with TGF-beta and TNF-alpha |
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Species: | Human (Homo sapiens) |
Library ID: | CNhs14490 |
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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CAGE Accession numbers | ||||||||||||||||||||||||||||||||||||||||||||||
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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: CNhs14490This 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: CNhs14490This 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: CNhs14490
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
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