FF:14382-156B8: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| (4 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
{{f5samples | {{f5samples | ||
|DRA_sample_Accession=CAGE@SAMD00011634 | |DRA_sample_Accession=CAGE@SAMD00011634 | ||
|accession_numbers=CAGE;DRX016549;DRR018322;DRZ003163;DRZ003169 | |accession_numbers=CAGE;DRX016549;DRR018322;DRZ003163;DRZ003169;DRZ008227;DRZ008233 | ||
|ancestors_in_anatomy_facet= | |ancestors_in_anatomy_facet= | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0002371,CL:0000034,CL:0002248 | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0002371,CL:0000034,CL:0002248 | ||
| Line 47: | Line 47: | ||
|is_a=FF:0000210;;FF:0300101 | |is_a=FF:0000210;;FF:0300101 | ||
|is_obsolete= | |is_obsolete= | ||
|library_id= | |library_id=CNhs14216 | ||
|library_id_phase_based=2: | |library_id_phase_based=2: | ||
|microRNAs= | |||
|microRNAs_nn= | |||
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;14382 | |||
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;14382 | |||
|name=hIPS, biol_rep3 | |name=hIPS, biol_rep3 | ||
|namespace= | |namespace= | ||
| Line 90: | Line 94: | ||
|top_motifs= | |top_motifs= | ||
|xref= | |xref= | ||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:14382-156B8;search_select_hide=table117:FF:14382-156B8 | |||
}} | }} | ||
Latest revision as of 19:08, 4 June 2020
| Name: | hIPS, biol_rep3 |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | CNhs14216 |
| Sample type: | time courses |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| ZENBU report : | link |
| Additional information | ||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
| CAGE Accession numbers | ||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| 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: CNhs14216This 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: CNhs14216This 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: CNhs14216
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
FF:0000210 human sample
FF:0300101 hIPS 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)
0000003 (native cell)
0000723 (somatic stem cell)
0002371 (somatic cell)
0000034 (stem cell)
0002248 (pluripotent stem cell)
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
