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Difference between revisions of "FF:13547-145I1"

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|ancestors_in_ff_facet=FF:0000210,FF:0000101,FF:0000001,FF:0000367,FF:0200010,FF:0200008
 
|ancestors_in_ff_facet=FF:0000210,FF:0000101,FF:0000001,FF:0000367,FF:0200010,FF:0200008
 
|data_phase=2
 
|data_phase=2
 +
|datafreeze_phase=2
 
|has_quality=
 
|has_quality=
 
|id=FF:13547-145I1
 
|id=FF:13547-145I1
 
|is_a=FF:0000210;;FF:0000367;;FF:0200008
 
|is_a=FF:0000210;;FF:0000367;;FF:0200008
 +
|library_id=CNhs14413
 
|library_id_phase_based=2:CNhs14413
 
|library_id_phase_based=2:CNhs14413
|name=293SLAM rinderpest infection, 12hr, biol_rep1
+
|name="293SLAM rinderpest infection, 12hr, biol_rep1"
 
|part_of=
 
|part_of=
 
|profile_cagescan=
 
|profile_cagescan=
|profile_hcage=CNhs14413,LSID1292,release018,COMPLETED
+
|profile_hcage="CNhs14413,LSID1292,release018,COMPLETED"
 
|profile_rnaseq=
 
|profile_rnaseq=
 
|profile_srnaseq=
 
|profile_srnaseq=

Revision as of 11:56, 27 November 2014


Name:"293SLAM rinderpest infection, 12hr, biol_rep1"
Species:Human (Homo sapiens)
Library ID:CNhs14413
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainUNDEFINED_STRAIN
tissueUNDEFINED_TISSUE_TYPE
dev stageUNDEFINED_DEV_STAGE
sexUNDEFINED_SEX_TYPE
ageNA
cell typeUNDEFINED_CELL_TYPE
cell line293SLAM
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
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





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: "CNhs14413This 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: "CNhs14413This 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: "CNhs14413


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

DOID: Disease
4 (disease)
0050117 (disease by infectious agent)

FF: FANTOM5
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000367 (12 hr sample)
0200010 (rinderpest infection sample)
0200008 (293SLAM rinderpest infection 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

NA