Difference between revisions of "FF:11502-119F8"
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{{f5samples | {{f5samples | ||
|DRA_sample_Accession=CAGE@SAMD00005807 | |DRA_sample_Accession=CAGE@SAMD00005807 | ||
| − | |accession_numbers=CAGE;DRX008335;DRR009207;DRZ000632;DRZ002017 | + | |accession_numbers=CAGE;DRX008335;DRR009207;DRZ000632;DRZ002017;DRZ011982;DRZ013367 |
|ancestors_in_anatomy_facet= | |ancestors_in_anatomy_facet= | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000075,CL:0000066,CL:0002371,CL:0000325,CL:0000147,CL:0000710,CL:0000255,CL:0002077,CL:0000148,CL:0002566 | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000075,CL:0000066,CL:0002371,CL:0000325,CL:0000147,CL:0000710,CL:0000255,CL:0002077,CL:0000148,CL:0002566 | ||
| Line 52: | Line 52: | ||
|microRNAs= | |microRNAs= | ||
|microRNAs_nn= | |microRNAs_nn= | ||
| − | |microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/ | + | |microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11502 |
| − | |microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/ | + | |microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11502 |
|name=Melanocyte - dark, donor1 | |name=Melanocyte - dark, donor1 | ||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
Latest revision as of 11:41, 10 August 2017
| Name: | Melanocyte - dark, donor1 |
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| Species: | Human (Homo sapiens) |
| Library ID: | CNhs12591 |
| Sample type: | primary cells |
| Genomic View: | UCSC |
| MicroRNAs: | Including candidate novel miRNAs(CAGE samples) Excluding candidate novel miRNAs(CAGE samples) |
| 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: CNhs12591This 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: CNhs12591This 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: CNhs12591
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000089 human dark melanocyte 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)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000325 (stuff accumulating cell)
0000147 (pigment cell)
0000710 (neurecto-epithelial cell)
0000255 (eukaryotic cell)
0002077 (ecto-epithelial cell)
0000148 (melanocyte)
0002566 (dark melanocyte)
FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000089 (human dark melanocyte 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:0000133 (neurectodermal cell)
CL:0000221 (ectodermal cell)
