Template:F5samples

Name:	{{{name}}}
Species:	{{{sample_species}}}
Sample type:	{{{sample_category}}}
Genomic View:	zenbu , UCSC

Library id:
Template

Additional information

Sample information strain: {{{sample_strain}}} tissue: {{{sample_tissue}}} dev_stage: {{{sample_dev_stage}}} sex: {{{sample_sex}}} age: {{{sample_age}}} ethnicity: {{{sample_ethnicity}}} cell_type: {{{sample_cell_type}}} cell_line: {{{sample_cell_line}}} collaboration: {{{sample_collaboration}}} Experimental condition: {{{sample_experimental_condition}}} disease: {{{sample_disease}}} cell_lot; {{{sample_cell_lot}}} cell_catalog: {{{sample_cell_catalog}}} donor(cell lot): {{{sample_donor(cell lot)}}} company: {{{sample_company}}} Note: {{{sample_note}}} Transcriptome profiling hCAGE: {{{profile_hcage}}} RNA-seq: {{{profile_rnaseq}}} smallRNA seq: {{{profile_srnaseq}}} nanoCAGEscan: {{{profile_cagescan}}} RNA information sample_id: {{{sample_id}}} tube_id: {{{rna_tube_id}}} box: {{{rna_box}}} position: {{{rna_position}}} tube_id: {{{rna_tube_id}}} lot_number: {{{rna_lot_number}}} catalog_number: {{{rna_catalog_number}}} RIN: {{{rna_rin}}} OD260/230: {{{rna_od260/230}}} OD260/280: {{{rna_od260/280}}} sample_type: {{{rna_sample_type}}} weight_ug: {{{rna_weight_ug}}} concentration: {{{rna_concentration}}} extraction_protocol:(Details) {{{rna_extraction_protocol}}}

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. <br>Analyst:NA <br><br>link to dataset.<br>data
Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data

no result for this sample

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

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JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: {{{profile_hcage}}}This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>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<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: {{{profile_hcage}}}

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
NA

DOID: Disease
NA

UBERON: Anatomy
NA

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

Property "Sample seq library id" (as page type) with input value "{{{profile_hcage}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.