Personal tools

FF:13605-146F5: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |ancestors_in_anatomy_facet= |ancestors_in_cell_lineage_facet= |ancestors_in_disease_facet= |ancestors_in_ff_facet= |has_quality= |id=FF:13605-146F5 |is_a= ...")
 
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=
|DRA_sample_Accession=CAGE@SAMD00022221
|ancestors_in_cell_lineage_facet=
|accession_numbers=CAGE;DRX024303;DRR026708;DRZ005960;DRZ006740;DRZ010575;DRZ011233
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0000483,UBERON:0000479,UBERON:0001007,UBERON:0000055,UBERON:0001281,UBERON:0000064,UBERON:0004119,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0005911,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0009569,UBERON:0002368,UBERON:0000353,UBERON:0003497,UBERON:0003909,UBERON:0005177,UBERON:0002365,UBERON:0007500,UBERON:0001981,UBERON:0005172,UBERON:0006925,UBERON:0002049,UBERON:0002530,UBERON:0003835,UBERON:0003513,UBERON:0010317,UBERON:0007798,UBERON:0005173,UBERON:0004535,UBERON:0002417,UBERON:0000949,UBERON:0001280,UBERON:0004647,UBERON:0002330,UBERON:0004537,UBERON:0000916,UBERON:0002423,UBERON:0001009
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000213,CL:0002078,CL:0000215,CL:0000255,CL:0000115
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=
|ancestors_in_ff_facet=FF:0000101,FF:0000103,FF:0000001,FF:0000375,FF:0200012,FF:0200013
|data_phase=2
|datafreeze_phase=2
|ffid_belonging_in_development=CL:0000222,UBERON:0002532,UBERON:0006595,UBERON:0006603,UBERON:0004872,UBERON:0006965,UBERON:0010316
|has_quality=
|has_quality=
|id=FF:13605-146F5
|id=FF:13605-146F5
|is_a=
|is_a=CL:0000115;;FF:0000103;;FF:0000375;;FF:0200013;;UBERON:0001281
|library_id=CNhs14405
|library_id_phase_based=2:CNhs14405
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;13605
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13605
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.LQhCAGE/liver%2520sinusoidal%2520endothelial%2520cells%252c%2520partial%2520hepatectomy%252c%252048hr%252c%2520biol_rep2.CNhs14405.13605-146F5.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.LQhCAGE/liver%2520sinusoidal%2520endothelial%2520cells%252c%2520partial%2520hepatectomy%252c%252048hr%252c%2520biol_rep2.CNhs14405.13605-146F5.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.LQhCAGE/liver%2520sinusoidal%2520endothelial%2520cells%252c%2520partial%2520hepatectomy%252c%252048hr%252c%2520biol_rep2.CNhs14405.13605-146F5.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.LQhCAGE/liver%2520sinusoidal%2520endothelial%2520cells%252c%2520partial%2520hepatectomy%252c%252048hr%252c%2520biol_rep2.CNhs14405.13605-146F5.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.LQhCAGE/liver%2520sinusoidal%2520endothelial%2520cells%252c%2520partial%2520hepatectomy%252c%252048hr%252c%2520biol_rep2.CNhs14405.13605-146F5.mm9.nobarcode.rdna.fa.gz
|name=liver sinusoidal endothelial cells, partial hepatectomy, 48hr, biol_rep2
|name=liver sinusoidal endothelial cells, partial hepatectomy, 48hr, biol_rep2
|part_of=
|part_of=
Line 26: Line 42:
|rna_weight_ug=1.17
|rna_weight_ug=1.17
|sample_age=
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=UNDEFINED_CELL_LINE
|sample_cell_line=UNDEFINED_CELL_LINE
Line 43: Line 60:
|sample_strain=UNDEFINED_STRAIN
|sample_strain=UNDEFINED_STRAIN
|sample_tissue=UNDEFINED_TISSUE_TYPE
|sample_tissue=UNDEFINED_TISSUE_TYPE
|timecourse=Liver_regeneration
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13605-146F5;search_select_hide=table117:13605-146F5
}}
}}

Latest revision as of 19:03, 4 June 2020


Name:liver sinusoidal endothelial cells, partial hepatectomy, 48hr, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs14405
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainUNDEFINED_STRAIN
tissueUNDEFINED_TISSUE_TYPE
dev stageUNDEFINED_DEV_STAGE
sexUNDEFINED_SEX_TYPE
ageNA
cell typeliver sinusoidal endothelial cell
cell lineUNDEFINED_CELL_LINE
companyNA
collaborationUNDEFINED_COLLABORATION
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00022221
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14405 CAGE DRX024303 DRR026708
Accession ID Mm9

Library idBAMCTSS
CNhs14405 DRZ005960 DRZ006740
Accession ID Mm10

Library idBAMCTSS
CNhs14405 DRZ010575 DRZ011233
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
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>data

CNhs14405



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: CNhs14405This 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: CNhs14405This 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: CNhs14405


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000213 (lining cell)
0002078 (meso-epithelial cell)
0000215 (barrier cell)
0000255 (eukaryotic cell)
0000115 (endothelial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0000483 (epithelium)
0000479 (tissue)
0001007 (digestive system)
0000055 (vessel)
0001281 (hepatic sinusoid)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0005911 (endo-epithelium)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0000353 (parenchyma)
0003497 (abdomen blood vessel)
0003909 (sinusoid)
0005177 (trunk region element)
0002365 (exocrine gland)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0005172 (abdomen element)
0006925 (digestive gland)
0002049 (vasculature)
0002530 (gland)
0003835 (abdominal segment blood vessel)
0003513 (trunk blood vessel)
0010317 (germ layer / neural crest derived structure)
0007798 (vascular system)
0005173 (abdominal segment element)
0004535 (cardiovascular system)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0001280 (liver parenchyma)
0004647 (liver lobule)
0002330 (exocrine system)
0004537 (blood vasculature)
0000916 (abdomen)
0002423 (hepatobiliary system)
0001009 (circulatory system)

FF: FANTOM5
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000375 (48 hr sample)
0200012 (real operation sample)
0200013 (partial hepatectomy 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
CL:0000222 (mesodermal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
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:13605-146F5&oldid=4578038"