Personal tools

FF:10361-105F1: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021170
|accession_numbers=CAGE;DRX023562;DRR025957;DRZ004382;DRZ005209;DRZ009123;DRZ009950
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0001896,UBERON:0000479,UBERON:0007221,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000092,UBERON:0000063,UBERON:0000481,UBERON:0000105,UBERON:0000000,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0004733,UBERON:0004732,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0000104,UBERON:0000066,UBERON:0002298,UBERON:0002028,UBERON:0005290,UBERON:0000112
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0001896,UBERON:0000479,UBERON:0007221,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000092,UBERON:0000063,UBERON:0000481,UBERON:0000105,UBERON:0000000,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0004733,UBERON:0004732,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0000104,UBERON:0000066,UBERON:0002298,UBERON:0002028,UBERON:0005290,UBERON:0000112
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
Line 8: Line 10:
|creation_date=
|creation_date=
|data_phase=2
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0000955;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001016;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001896;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0002028;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0002298
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316
|fonse_cell_line=
|fonse_cell_line=
Line 37: Line 41:
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/medulla%2520oblongata%252c%2520newborn%252c%2520donor10223.CNhs14079.10361-105F1.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/medulla%2520oblongata%252c%2520newborn%252c%2520donor10223.CNhs14079.10361-105F1.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/medulla%2520oblongata%252c%2520newborn%252c%2520donor10223.CNhs14079.10361-105F1.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/medulla%2520oblongata%252c%2520newborn%252c%2520donor10223.CNhs14079.10361-105F1.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/medulla%2520oblongata%252c%2520newborn%252c%2520donor10223.CNhs14079.10361-105F1.hg38.nobarcode.ctss.bed.gz
|id=FF:10361-105F1
|id=FF:10361-105F1
|is_a=EFO:0001372;;FF:0000004;;FF:0000210;;UBERON:0001896;;UBERON:0007221
|is_a=EFO:0001372;;FF:0000004;;FF:0000210;;UBERON:0001896;;UBERON:0007221
|is_obsolete=
|is_obsolete=
|library_id_phase_based=2:CNhs14079
|library_id=CNhs14079
|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;10361
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10361
|name=medulla oblongata, newborn, donor10223
|name=medulla oblongata, newborn, donor10223
|namespace=
|namespace=
Line 82: Line 96:
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10361-105F1;search_select_hide=table117:FF:10361-105F1
}}
}}

Latest revision as of 13:58, 3 June 2020

Name:medulla oblongata, newborn, donor10223
Species:Human (Homo sapiens)
Library ID:CNhs14079
Sample type:tissues
Genomic View: UCSC
FANTOM CAT:1, 2, 3, 4, 5
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuemedulla oblongata
dev stageNA
sexmale
age0
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021170
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14079 CAGE DRX023562 DRR025957
Accession ID Hg19

Library idBAMCTSS
CNhs14079 DRZ004382 DRZ005209
Accession ID Hg38

Library idBAMCTSS
CNhs14079 DRZ009123 DRZ009950
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: CNhs14079This 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: CNhs14079This 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: CNhs14079


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)
0000955 (brain)
0001896 (medulla oblongata)
0000479 (tissue)
0007221 (neonate stage)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000092 (post-embryonic stage)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000105 (life cycle stage)
0000000 (processual entity)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0000104 (life cycle)
0000066 (fully formed stage)
0002298 (brainstem)
0002028 (hindbrain)
0005290 (myelencephalon)
0000112 (juvenile stage)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000004 (tissue 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:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:10361-105F1&oldid=4575991"