Personal tools

FF:10190-103E1: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(6 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005230
|DRA_sample_Accession=CAGE@SAMD00005230
|accession_numbers=CAGE;DRX008621;DRR009493;DRZ000918;DRZ002303
|accession_numbers=CAGE;DRX008621;DRR009493;DRZ000918;DRZ002303;DRZ012268;DRZ013653
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001637,UBERON:0000483,UBERON:0000479,UBERON:0000055,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0002049,UBERON:0010317,UBERON:0007798,UBERON:0004535,UBERON:0004572,UBERON:0004537,UBERON:0001009
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001637,UBERON:0000483,UBERON:0000479,UBERON:0000055,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0002049,UBERON:0010317,UBERON:0007798,UBERON:0004535,UBERON:0004572,UBERON:0004537,UBERON:0001009
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
Line 9: Line 9:
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=1
|data_phase=2
|datafreeze_phase=1
|datafreeze_phase=2
|def=
|def=
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0004872,UBERON:0006965,UBERON:0010316
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0004872,UBERON:0006965,UBERON:0010316
Line 40: Line 40:
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/artery%252c%2520adult.CNhs12843.10190-103E1.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/artery%252c%2520adult.CNhs12843.10190-103E1.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/artery%252c%2520adult.CNhs12843.10190-103E1.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/artery%252c%2520adult.CNhs12843.10190-103E1.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/artery%252c%2520adult.CNhs12843.10190-103E1.hg38.nobarcode.ctss.bed.gz
|id=FF:10190-103E1
|id=FF:10190-103E1
|is_a=EFO:0002091;;FF:0010190
|is_a=EFO:0002091;;FF:0010190
|is_obsolete=
|is_obsolete=
|library_id=CNhs12843
|library_id=CNhs12843
|library_id_phase_based=1:CNhs12843
|library_id_phase_based=2:CNhs12843
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10190
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10190
|name=artery, adult
|name=artery, adult
|namespace=FANTOM5
|namespace=FANTOM5
Line 50: Line 59:
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs12843,LSID973,release012,COMPLETED
|profile_hcage=CNhs12843,LSID973,release012,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|rna_box=103
|rna_box=103
Line 62: Line 71:
|rna_rin=
|rna_rin=
|rna_sample_type=
|rna_sample_type=
|rna_tube_id=103E1
|rna_tube_id=1.03E+03
|rna_weight_ug=10
|rna_weight_ug=10
|sample_age=27
|sample_age=27
Line 86: Line 95:
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10190-103E1;search_select_hide=table117:FF:10190-103E1
}}
}}

Latest revision as of 12:26, 3 June 2020


Name:artery, adult
Species:Human (Homo sapiens)
Library ID:CNhs12843
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexM
age27
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberR1234013-10
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005230
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12843 CAGE DRX008621 DRR009493
Accession ID Hg19

Library idBAMCTSS
CNhs12843 DRZ000918 DRZ002303
Accession ID Hg38

Library idBAMCTSS
CNhs12843 DRZ012268 DRZ013653
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload





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: CNhs12843This 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: CNhs12843This 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: CNhs12843


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)
0001637 (artery)
0000483 (epithelium)
0000479 (tissue)
0000055 (vessel)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003509 (arterial blood vessel)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0002049 (vasculature)
0010317 (germ layer / neural crest derived structure)
0007798 (vascular system)
0004535 (cardiovascular system)
0004572 (arterial system)
0004537 (blood vasculature)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010190 (human artery - 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:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0006965 (vascular cord)
UBERON:0010316 (germ layer / neural crest)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:10190-103E1&oldid=4575926"