Template:F5samples: Difference between revisions
From FANTOM5_SSTAR
mNo edit summary |
mNo edit summary |
||
Line 28: | Line 28: | ||
<tr><th scope="row" align="right">Name:</th><td>[[name::{{{name}}}]]</td></tr> | <tr><th scope="row" align="right">Name:</th><td>[[name::{{{name}}}]]</td></tr> | ||
<tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr> | <tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr> | ||
<tr><th scope="row" align="right">[[Property:Sample_category|Sample type]]:</th><td>{{{sample_category}}}</td></tr> | <tr><th scope="row" align="right">[[Property:Sample_category|Sample type]]:</th><td>{{{sample_category}}}</td></tr> | ||
<tr><th scope="row" align="right">Genomic View:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [https://fantom5-collaboration.gsc.riken.jp/ucsc/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></table> | <tr><th scope="row" align="right">Genomic View:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [https://fantom5-collaboration.gsc.riken.jp/ucsc/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">[[Property:Library_id|Library]]:</th><td>{{LibraryIds|{{{library_id_phase_based}}}}}</td></tr></table> | |||
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto" | {|class="wikitable mw-collapsible mw-collapsed" style="width:auto" | ||
! Additional information | ! Additional information | ||
Line 446: | Line 446: | ||
<br><br> | <br><br> | ||
{{#arraydefine:libids_array|{{#arraymap:{{library_id_phase_based}}|;|$|{{#explode:$|:|1}}}}|,}} | |||
{{#vardefine:libraryidsall|{{#arrayprint:libids_array|!}}}} | |||
{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}| | {{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}| | ||
{{#set:sample_category={{{sample_category}}}}} | {{#set:sample_category={{{sample_category}}}}} | ||
{{#arraymap:{{ | {{#arraymap:{{#var:libraryidsall}}|!|$ | ||
|{{#set:Library | |{{#set:Library id=$}} | ||
}} | }} | ||
Revision as of 14:36, 17 June 2014
Name: | {{{name}}} | ||
---|---|---|---|
Species: | {{{sample_species}}} | ||
Sample type: | {{{sample_category}}} | ||
Genomic View: | zenbu , UCSC | ||
Library: |
|
Additional information | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
Transcriptome profiling
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. <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 "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.