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{{f5samples
 
{{f5samples
 +
|DRA_sample_Accession=CAGE@SAMD00021346
 +
|accession_numbers=CAGE;DRX022999;DRR025338;DRZ003763;DRZ004646;DRZ008504;DRZ009387
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000055,UBERON:0004111,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002049,UBERON:0007798,UBERON:0001473,UBERON:0002465,UBERON:0004535,UBERON:0004536,UBERON:0006558,UBERON:0002193,UBERON:0002405,UBERON:0001009
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000055,UBERON:0004111,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002049,UBERON:0007798,UBERON:0001473,UBERON:0002465,UBERON:0004535,UBERON:0004536,UBERON:0006558,UBERON:0002193,UBERON:0002405,UBERON:0001009
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002139,CL:0000213,CL:0002078,CL:0000215,CL:0000255,CL:0000115,CL:0002138
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002139,CL:0000213,CL:0002078,CL:0000215,CL:0000255,CL:0000115,CL:0002138
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|datafreeze_phase=2
 
|datafreeze_phase=2
 
|def=
 
|def=
 +
|donor= biol_rep3 (MM XXII - 4)
 
|ffid_belonging_in_development=CL:0000222,CL:0005022
 
|ffid_belonging_in_development=CL:0000222,CL:0005022
 
|fonse_cell_line=
 
|fonse_cell_line=
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|fonse_treatment_closure=EFO:0000369,FF:0000341,FF:0000413,FF:12507-133A5
 
|fonse_treatment_closure=EFO:0000369,FF:0000341,FF:0000413,FF:12507-133A5
 
|has_quality=
 
|has_quality=
 +
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Lymphatic%2520Endothelial%2520cells%2520response%2520to%2520VEGFC%252c%252000hr45min%252c%2520biol_rep3%2520%2528MM%2520XXII%2520-%25204%2529.CNhs13279.12507-133A5.hg19.nobarcode.bam
 +
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Lymphatic%2520Endothelial%2520cells%2520response%2520to%2520VEGFC%252c%252000hr45min%252c%2520biol_rep3%2520%2528MM%2520XXII%2520-%25204%2529.CNhs13279.12507-133A5.hg19.ctss.bed.gz
 +
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Lymphatic%2520Endothelial%2520cells%2520response%2520to%2520VEGFC%252c%252000hr45min%252c%2520biol_rep3%2520%2528MM%2520XXII%2520-%25204%2529.CNhs13279.12507-133A5.hg19.nobarcode.rdna.fa.gz
 +
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Lymphatic%2520Endothelial%2520cells%2520response%2520to%2520VEGFC%252c%252000hr45min%252c%2520biol_rep3%2520%2528MM%2520XXII%2520-%25204%2529.CNhs13279.12507-133A5.hg38.nobarcode.bam
 +
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Lymphatic%2520Endothelial%2520cells%2520response%2520to%2520VEGFC%252c%252000hr45min%252c%2520biol_rep3%2520%2528MM%2520XXII%2520-%25204%2529.CNhs13279.12507-133A5.hg38.nobarcode.ctss.bed.gz
 
|id=FF:12507-133A5
 
|id=FF:12507-133A5
 
|is_a=EFO:0002091;;FF:0000413
 
|is_a=EFO:0002091;;FF:0000413
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|library_id=CNhs13279
 
|library_id=CNhs13279
 
|library_id_phase_based=2:CNhs13279
 
|library_id_phase_based=2:CNhs13279
|name="Lymphatic Endothelial cells response to VEGFC, 00hr45min, biol_rep3 (MM XXII - 4)"
+
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;12507
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;12507
 +
|name=Lymphatic Endothelial cells response to VEGFC
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 
|profile_cagescan=,,,
 
|profile_cagescan=,,,
|profile_hcage="CNhs13279,LSID1020,release013,COMPLETED"
+
|profile_hcage=CNhs13279,LSID1020,release013,COMPLETED
 
|profile_rnaseq=
 
|profile_rnaseq=
|profile_srnaseq=",,,"
+
|profile_srnaseq=,,,
 
|rna_box=133
 
|rna_box=133
 
|rna_catalog_number=
 
|rna_catalog_number=
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|sample_cell_line=
 
|sample_cell_line=
 
|sample_cell_lot=
 
|sample_cell_lot=
|sample_cell_type="endothelial cell, lymphatic"
+
|sample_cell_type=endothelial cell, lymphatic
|sample_collaboration="Michael Detmar (Swiss Federal Institute of Technology, ETH Zurich)"
+
|sample_collaboration=Michael Detmar (Swiss Federal Institute of Technology, ETH Zurich)
 
|sample_company=
 
|sample_company=
 
|sample_description=
 
|sample_description=
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|sample_strain=
 
|sample_strain=
 
|sample_tissue=lymph node
 
|sample_tissue=lymph node
|timecourse=human_Lymphatic_Endothelial_cells_response_to_VEGFC
+
|time= 00hr45min
 +
|timecourse=Lymphatic_EC_response_to_VEGFC
 
|top_motifs=
 
|top_motifs=
 
|xref=
 
|xref=
 
}}
 
}}

Latest revision as of 12:47, 10 August 2017


Name:Lymphatic Endothelial cells response to VEGFC
Species:Human (Homo sapiens)
Library ID:CNhs13279
Sample type:time courses
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelymph node
dev stageNA
sexNA
ageNA
cell typeendothelial cell, lymphatic
cell lineNA
companyNA
collaborationMichael Detmar (Swiss Federal Institute of Technology, ETH Zurich)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00021346
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13279 CAGE DRX022999 DRR025338
Accession ID Hg19

Library idBAMCTSS
CNhs13279 DRZ003763 DRZ004646
Accession ID Hg38

Library idBAMCTSS
CNhs13279 DRZ008504 DRZ009387
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.
Analyst:NA

link to dataset.
data
No results for this sample

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data
no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs13279This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs13279This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs13279


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002139 (endothelial cell of vascular tree)
0000213 (lining cell)
0002078 (meso-epithelial cell)
0000215 (barrier cell)
0000255 (eukaryotic cell)
0000115 (endothelial cell)
0002138 (endothelial cell of lymphatic vessel)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000055 (vessel)
0004111 (anatomical conduit)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002049 (vasculature)
0007798 (vascular system)
0001473 (lymphatic vessel)
0002465 (lymphoid system)
0004535 (cardiovascular system)
0004536 (lymph vasculature)
0006558 (lymphatic part of lymphoid system)
0002193 (hemolymphoid system)
0002405 (immune system)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000046 (human endothelial cell sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000049 (human lymphatic endothelial cell sample)
0000341 (Vegfc treatment sample)
0000347 (45 minutes sample)
0000413 (human Lymphatic Endothelial cells 45min after VEGFC treatment sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

CL:0000222 (mesodermal cell)
CL:0005022 (vascular lymphangioblast)