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<tr><th scope="row" align="right">Genomic View:</th><td>[http://fantom.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [http://genome.ucsc.edu/cgi-bin/hgTracks?db={{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | hg19 | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mm9 | }}{{#ifeq: {{{sample_species}}} | Rat (Rattus rattus) |  rn4 | }}{{#ifeq: {{{sample_species}}} | Dog (Canis lupus familaris) | canFam2 | }}{{#ifeq: {{{sample_species}}} | Chicken (Gallus gallus) | galGal3 | }}&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC] </td></tr>
<tr><th scope="row" align="right">Genomic View:</th><td>[http://fantom.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [http://genome.ucsc.edu/cgi-bin/hgTracks?db={{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | hg19 | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mm9 | }}{{#ifeq: {{{sample_species}}} | Rat (Rattus rattus) |  rn4 | }}{{#ifeq: {{{sample_species}}} | Dog (Canis lupus familaris) | canFam2 | }}{{#ifeq: {{{sample_species}}} | Chicken (Gallus gallus) | galGal3 | }}&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC] </td></tr>
{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}|ttp}}|
{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}|ttp}}|
<tr><th scope="row" align="right">MicroRNAs:</th><td>[{{{microRNAs_novel_cage}}} Novel-CAGE]&nbsp;[{{{microRNAs_novel_cage}}} Novel-sRNA]&nbsp;&nbsp;{{#ifexpr: {{#pos:{{{microRNAs_nn}}}|ttp}}| [{{{microRNAs_nn}}} Non-novel-CAGE]&nbsp;[{{{microRNAs_nn}}} Non-novel-sRNA]|}}  </td></tr>|}}
<tr><th scope="row" align="right">MicroRNAs:</th><td>Novel<span style="font-size:xx-small;">([{{{microRNAs_novel_cage}}} CAGE samples],&nbsp;[{{{microRNAs_novel_cage}}} sRNA samples])</span>&nbsp;&nbsp;{{#ifexpr: {{#pos:{{{microRNAs_nonnovel_cage}}}|ttp}}| Non-novel<span style="font-size:xx-small;">([{{{microRNAs_nn}}} CAGE samples],&nbsp;[{{{microRNAs_nn}}} sRNA samples])</span>|}}  </td></tr>|}}
{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}|ttp}}|
<tr><th scope="row" align="right">MicroRNAs:</th><td>Novel<span style="font-size:xx-small;">([{{{microRNAs_novel_cage}}} CAGE samples],&nbsp;[{{{microRNAs_novel_cage}}} sRNA samples])</span>&nbsp;&nbsp;{{#ifexpr: {{#pos:{{{microRNAs_nn}}}|ttp}}| Non-novel<span style="font-size:xx-small;">([{{{microRNAs_nn}}} CAGE samples],&nbsp;[{{{microRNAs_nn}}} sRNA samples])</span>|}}  </td></tr>|}}
<tr><th scope="row" align="right">CAGEd-oPOSSUM:</th><td>[http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/{{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | human | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mouse | }}/{{{id}}}/results.html link]  </td></tr></table>
<tr><th scope="row" align="right">CAGEd-oPOSSUM:</th><td>[http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/{{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | human | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mouse | }}/{{{id}}}/results.html link]  </td></tr></table>
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Revision as of 17:28, 13 February 2017

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 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


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


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 "Timecourse" (as page type) with input value "{{{timecourse}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.



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