Personal tools

Template:F5samples

From FANTOM5_SSTAR

Revision as of 15:15, 29 June 2016 by A-Kondo (Talk | contribs)

Jump to: navigation, search

Name:{{{name}}}
Species:{{{sample_species}}}
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View:zenbu , UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strain{{{sample_strain}}}
tissue{{{sample_tissue}}}
dev stage{{{sample_dev_stage}}}
sex{{{sample_sex}}}
age{{{sample_age}}}
cell type{{{sample_cell_type}}}
cell line{{{sample_cell_line}}}
company{{{sample_company}}}
collaboration{{{sample_collaboration}}}
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number{{{rna_lot_number}}}
catalog number{{{rna_catalog_number}}}
sample type{{{rna_sample_type}}}
extraction protocol (Details){{{rna_extraction_protocol}}}



Co-expression clusters with enriched expression in this sample

Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: {{{profile_hcage}}}This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifs
Summary: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: {{{profile_hcage}}}This sample isn't target for the analysis

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

library id: {{{profile_hcage}}}


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
NA

DOID: Disease
NA

UBERON: Anatomy
NA

FF: FANTOM5
NA

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



















"{{{timecourse}}}" cannot be used as a page name in this wiki.



"{{{profile_hcage}}}" cannot be used as a page name in this wiki.
"{{{sample_timecourse}}}" cannot be used as a page name in this wiki.