FF:13588-146D6: Difference between revisions
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{{f5samples | {{f5samples | ||
|DRA_sample_Accession=CAGE@SAMD00022204 | |||
|accession_numbers=CAGE;DRX024283;DRR026688;DRZ005940;DRZ006720;DRZ010555;DRZ011213 | |||
|ancestors_in_anatomy_facet= | |ancestors_in_anatomy_facet= | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
| Line 5: | Line 7: | ||
|ancestors_in_ff_facet= | |ancestors_in_ff_facet= | ||
|data_phase=2 | |data_phase=2 | ||
|datafreeze_phase=2 | |||
|has_quality= | |has_quality= | ||
|id=FF:13588-146D6 | |id=FF:13588-146D6 | ||
|is_a= | |is_a= | ||
|library_id=CNhs14455 | |||
|library_id_phase_based=2:CNhs14455 | |library_id_phase_based=2:CNhs14455 | ||
|microRNAs= | |||
|microRNAs_nn= | |||
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;13588 | |||
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13588 | |||
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/hepatocytes%252c%2520partial%2520hepatectomy%252c%252030hr%252c%2520biol_rep3.CNhs14455.13588-146D6.mm10.nobarcode.bam | |||
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/hepatocytes%252c%2520partial%2520hepatectomy%252c%252030hr%252c%2520biol_rep3.CNhs14455.13588-146D6.mm10.nobarcode.ctss.bed.gz | |||
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/hepatocytes%252c%2520partial%2520hepatectomy%252c%252030hr%252c%2520biol_rep3.CNhs14455.13588-146D6.mm9.nobarcode.bam | |||
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/hepatocytes%252c%2520partial%2520hepatectomy%252c%252030hr%252c%2520biol_rep3.CNhs14455.13588-146D6.mm9.ctss.bed.gz | |||
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/hepatocytes%252c%2520partial%2520hepatectomy%252c%252030hr%252c%2520biol_rep3.CNhs14455.13588-146D6.mm9.nobarcode.rdna.fa.gz | |||
|name=hepatocytes, partial hepatectomy, 30hr, biol_rep3 | |name=hepatocytes, partial hepatectomy, 30hr, biol_rep3 | ||
|part_of= | |part_of= | ||
| Line 47: | Line 60: | ||
|sample_tissue=UNDEFINED_TISSUE_TYPE | |sample_tissue=UNDEFINED_TISSUE_TYPE | ||
|timecourse=Liver_regeneration | |timecourse=Liver_regeneration | ||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13588-146D6;search_select_hide=table117:13588-146D6 | |||
}} | }} | ||
Latest revision as of 19:02, 4 June 2020
| Name: | hepatocytes, partial hepatectomy, 30hr, biol_rep3 |
|---|---|
| Species: | Mouse (Mus musculus) |
| Library ID: | CNhs14455 |
| 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>data
CNhs14455
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: CNhs14455This 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: CNhs14455This 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: CNhs14455
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
