FF:10192-103E3: Difference between revisions
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{{f5samples | {{f5samples | ||
|DRA_sample_Accession=CAGE@SAMD00005595 | |||
|accession_numbers=CAGE;DRX008624;DRR009496;DRZ000921;DRZ002306;DRZ012271;DRZ013656 | |||
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0002371,UBERON:0001474,UBERON:0000479,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0010317,UBERON:0002204,UBERON:0001434,UBERON:0002390,UBERON:0002193,UBERON:0002405 | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0002371,UBERON:0001474,UBERON:0000479,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0010317,UBERON:0002204,UBERON:0001434,UBERON:0002390,UBERON:0002193,UBERON:0002405 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
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|created_by= | |created_by= | ||
|creation_date= | |creation_date= | ||
|datafreeze_phase= | |data_phase=2 | ||
|datafreeze_phase=2 | |||
|def= | |def= | ||
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316 | |ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316 | ||
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|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/bone%2520marrow%252c%2520adult.CNhs12845.10192-103E3.hg19.nobarcode.bam | |||
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/bone%2520marrow%252c%2520adult.CNhs12845.10192-103E3.hg19.ctss.bed.gz | |||
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/bone%2520marrow%252c%2520adult.CNhs12845.10192-103E3.hg19.nobarcode.rdna.fa.gz | |||
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/bone%2520marrow%252c%2520adult.CNhs12845.10192-103E3.hg38.nobarcode.bam | |||
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/bone%2520marrow%252c%2520adult.CNhs12845.10192-103E3.hg38.nobarcode.ctss.bed.gz | |||
|id=FF:10192-103E3 | |id=FF:10192-103E3 | ||
|is_a=EFO:0002091;;FF:0010192 | |is_a=EFO:0002091;;FF:0010192 | ||
|is_obsolete= | |is_obsolete= | ||
|library_id=CNhs12845 | |||
|library_id_phase_based=2:CNhs12845 | |||
|microRNAs= | |||
|microRNAs_nn= | |||
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10192 | |||
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10192 | |||
|name=bone marrow, adult | |name=bone marrow, adult | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
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|profile_cagescan=,,, | |profile_cagescan=,,, | ||
|profile_hcage=CNhs12845,LSID973,release012,COMPLETED | |profile_hcage=CNhs12845,LSID973,release012,COMPLETED | ||
|profile_rnaseq= | |profile_rnaseq= | ||
|profile_srnaseq=,,, | |profile_srnaseq=,,, | ||
|rna_box=103 | |rna_box=103 | ||
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|rna_rin= | |rna_rin= | ||
|rna_sample_type= | |rna_sample_type= | ||
|rna_tube_id= | |rna_tube_id=1.03E+05 | ||
|rna_weight_ug=10 | |rna_weight_ug=10 | ||
|sample_age= | |sample_age=27 | ||
|sample_category=tissues | |sample_category=tissues | ||
|sample_cell_catalog=NA | |sample_cell_catalog=NA | ||
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|sample_id=10192 | |sample_id=10192 | ||
|sample_note= | |sample_note= | ||
|sample_sex= | |sample_sex=M | ||
|sample_species=Human (Homo sapiens) | |sample_species=Human (Homo sapiens) | ||
|sample_strain= | |sample_strain= | ||
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|top_motifs= | |top_motifs= | ||
|xref= | |xref= | ||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10192-103E3;search_select_hide=table117:FF:10192-103E3 | |||
}} | }} |
Latest revision as of 12:26, 3 June 2020
Name: | bone marrow, adult |
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Species: | Human (Homo sapiens) |
Library ID: | CNhs12845 |
Sample type: | tissues |
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: CNhs12845This 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: CNhs12845This 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: CNhs12845
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
UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0002371 (bone marrow)
0001474 (bone element)
0000479 (tissue)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0010317 (germ layer / neural crest derived structure)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0002390 (hematopoietic system)
0002193 (hemolymphoid system)
0002405 (immune system)
FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010192 (human bone marrow - adult 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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)