Difference between revisions of "FF:12506-133A4"
From FANTOM5_SSTAR
| Line 12: | Line 12: | ||
|datafreeze_phase=2 | |datafreeze_phase=2 | ||
|def= | |def= | ||
| + | |donor= biol_rep3 (MM XXII - 3) | ||
|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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|library_id=CNhs13278 | |library_id=CNhs13278 | ||
|library_id_phase_based=2:CNhs13278 | |library_id_phase_based=2:CNhs13278 | ||
| − | |name=Lymphatic Endothelial cells response to VEGFC | + | |name=Lymphatic Endothelial cells response to VEGFC |
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
| Line 84: | Line 85: | ||
|sample_strain= | |sample_strain= | ||
|sample_tissue=lymph node | |sample_tissue=lymph node | ||
| + | |time= 00hr30min | ||
|timecourse=human_Lymphatic_Endothelial_cells_response_to_VEGFC | |timecourse=human_Lymphatic_Endothelial_cells_response_to_VEGFC | ||
|top_motifs= | |top_motifs= | ||
|xref= | |xref= | ||
}} | }} | ||
Revision as of 06:21, 9 January 2015
| Name: | Lymphatic Endothelial cells response to VEGFC |
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| Species: | Human (Homo sapiens) |
| Library ID: | CNhs13278 |
| Sample type: | time courses |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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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.
Analyst:NA
link to dataset.
dataNo 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: CNhs13278This 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: CNhs13278This 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: CNhs13278
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000412 human Lymphatic Endothelial cells 30min after VEGFC treatment sample
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)
0000346 (30 minutes sample)
0000412 (human Lymphatic Endothelial cells 30min 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)
