Template:F5samplesTest

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

Additional information

Transcriptome profiling hCAGE: {{{profile_hcage}}} RNA-seq: {{{profile_rnaseq}}} smallRNA seq: {{{profile_srnaseq}}} nanoCAGEscan: {{{profile_cagescan}}} 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}}} company: {{{sample_company}}} 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}}} External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] 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}}}

Details

Transcriptome profiling

hCAGE:	{{{profile_hcage}}}
RNA-seq:	{{{profile_rnaseq}}}
smallRNA seq:	{{{profile_srnaseq}}}
nanoCAGEscan:	{{{profile_cagescan}}}

Sample info

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}}}
company:	{{{sample_company}}}
donor(cell lot):	{{{sample_donor(cell lot)}}}
Note:	{{{sample_note}}}

RNA info

sample_id:	{{{sample_id}}}
tube_id:	{{{rna_tube_id}}}
box:	{{{rna_box}}}
position:	{{{rna_position}}}
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}}}
extraction_protocol:	{{{rna_extraction_protocol}}}
weight_ug:	{{{rna_weight_ug}}}
concentration:	{{{rna_concentration}}}

Parent ontology

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestors in ontology (non-development)

Connected ontology terms with is_a, part_of or located_in relathionship <br>Analyst: Hideya Kawaji

CL: Cell type

DOID: Disease
Property "Ancestors in disease facet" (as page type) with input value "{{{ancestors_in_disease_facet}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.

UBERON: Anatomy

FF: FANTOM5

Ancestors in ontology (development)

Connected ontology terms with develops_from, derives_from or preceded_by relathionship <br>Analyst: Hideya Kawaji