Difference between revisions of "Template:F5samples"
From FANTOM5_SSTAR
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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>Novel<span style="font-size:xx-small;">([{{{microRNAs_novel_cage}}} CAGE samples], [{{{microRNAs_novel_cage}}} sRNA samples])</span> {{#ifexpr: {{#pos:{{{microRNAs_nonnovel_cage}}}|ttp}}| Non-novel<span style="font-size:xx-small;">([{{{microRNAs_nn}}} CAGE samples], [{{{microRNAs_nn}}} sRNA samples])</span>|}} </td></tr>|}} | |
− | |||
− | <tr><th scope="row" align="right">MicroRNAs:</th><td>Novel<span style="font-size:xx-small;">([{{{microRNAs_novel_cage}}} CAGE samples], [{{{microRNAs_novel_cage}}} sRNA samples])</span> {{#ifexpr: {{#pos:{{{ | ||
<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> | ||
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto" | {|class="wikitable mw-collapsible mw-collapsed" style="width:auto" |
Revision as of 08:28, 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 | ||||||||||||||||||||||||||||
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Sample information
RNA information
|
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
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: {{{profile_hcage}}}This 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: {{{profile_hcage}}}This 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: {{{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
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.