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FANTOM5 SSTAR (Semantic catalog of Samples, Transcription initiation And Regulators) provide a way to explore samples, transcriptional initiations, and regulators analyzed in [http://fantom.gsc.riken.jp/5/ the FANTOM5 project]. If you have any questions or comments, please contact to fantom@gsc.riken.jp
== outline ==
<html><style>
*id: [[id::{{{id}}}]]
#front-table td { border-top: 1px solid #AAA; vertical-align:middle; padding: 0.5em; height: 85px; }
*name: [[name::{{{name}}}]]
#front-table th { text-align: left; padding: 2em 0 0.3em 0.5em; }
{{#if: {{{namespace}}} | *namespace: {{#show:{{FULLPAGENAME}}|?namespace}}|}}{{#if: {{{def}}} | *def: {{#show:{{FULLPAGENAME}}|?def}}|}}{{#if: {{{xref}}} | *xref: {{#show:{{FULLPAGENAME}}|?xref}}|}}
#front-table li { line-height: 1.2em; }
{{#if: {{{synonym}}} | *synonym: {{#show:{{FULLPAGENAME}}|?synonym}}|}}{{#if: {{{comment}}} | *comment: {{#show:{{FULLPAGENAME}}|?comment}}|}}{{#if: {{{alt_id}}} | *alt_id: {{#show:{{FULLPAGENAME}}|?alt_id}}|}}{{#if: {{{created_by}}} | *created_by: {{#show:{{FULLPAGENAME}}|?created_by}}|}}{{#if: {{{subset}}} | *subset: {{#show:{{FULLPAGENAME}}|?subset}}|}}{{#if: {{{obo_creation_date}}} | *creation_date: {{#show:{{FULLPAGENAME}}|?obo_creation_date}}|}}
#front-table tbody tr:nth-child(even) td, tbody tr.even td {
*CAGEd oPOSSUM: {{#if:{{{caged_opossum_human|}}}||{{#if:{{{caged_opossum_mouse|}}}||NA}}}}{{#if:{{{caged_opossum_human|}}}|[{{{caged_opossum_human}}} human]|}}{{#if:{{{caged_opossum_mouse|}}}|[{{{caged_opossum_mouse}}} mouse]|}}
background: #E5ECF9;
}
</style></html>
<table cellspacing="0" id="front-table">
<html>
<form method="get" action="/5/sstar/RB_SearchResults">
  <tr>
    <th ><b>Search genes</b></td>
    <th  colspan="2"><input type="text" name="sq" value="" style="width: 440px;"></td>
    <th ><input type="submit" value="search"></td>
  </tr>
</form>


  <tr> &nbsp; </tr>
== Ontology association ==
=== Parents ===
<table>
{{#if:{{{is_a}}}|<tr><th width=100 align="right">is_a:</th><td>{{#arraymap:{{{is_a}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{disjoint_from}}}|<tr><th width=100 align="right">disjoint_from:</th><td>{{#arraymap:{{{disjoint_from}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{union_of}}}|<tr><th width=100 align="right">union_of:</th><td>{{#arraymap:{{{union_of}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{derives_from}}}|<tr><th width=100 align="right">derives_from:</th><td>{{#arraymap:{{{derives_from}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{develops_from}}}|<tr><th width=100 align="right">develops_from:</th><td>{{#arraymap:{{{develops_from}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{has_quality}}}|<tr><th width=100 align="right">has_quality:</th><td>{{#arraymap:{{{has_quality}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{located_in}}}|<tr><th width=100 align="right">located_in:</th><td>{{#arraymap:{{{located_in}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{part_of}}}|<tr><th width=100 align="right">part_of:</th><td>{{#arraymap:{{{part_of}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}
</table>


  <tr>
=== Children  ===
    <th style="width: 120px;"></td>
<table>
    <th style="width: 300px;"></td>
{{#ask:[[is_a::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">is_a:</th><td>|outro=</td></tr>}}{{#ask:[[disjoint_from::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">disjoint_from:</th><td>|outro=</td></tr>}}{{#ask:[[adjacent_to::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">adjacent_to:</th><td>|outro=</td></tr>}}{{#ask:[[derives_from::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">derives_from:</th><td>|outro=</td></tr>}}{{#ask:[[develops_from::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">develops_from:</th><td>|outro=</td></tr>}}{{#ask:[[has_quality::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">has_quality:</th><td>|outro=</td></tr>}}{{#ask:[[located_in::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">located_in:</th><td>|outro=</td></tr>}}{{#ask:[[part_of::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">part_of:</th><td>|outro=</td></tr>}}
    <th style="width: 160px; padding-left: 19px;">Examples</td>
</table>
    <th style="width: 160px;">Browse</td>
  </tr></html>
<tr>
    <td>'''Time courses '''</td>
    <td>Promoters and enhancers activity in 19 human and 14 mouse time courses
covering a wide range of cell types and biological stimuli</td>
    <td style="width: 160px;"> <ul><li>[[Human_iPS_to_neuron_(Down's_syndrome)_1|Human iPS to neuron (Down's syndrome)]] </li></ul>   </td>
    <td>
[[Time_Courses_chart|Timecourses chart]]
 
</td>
  </tr>
 
  <tr>
    <td>'''Samples'''</td>
    <td> Details of profiled samples (incl. primary cells, cell lines, and tissues) </td>
    <td style="width: 160px;"> <ul><li>[[FF:11210-116A4|Smooth Muscle Cells - Aortic, donor0]] </li></ul>   </td>
    <td>
[[Browse_samples|human]]


[[Browse_samples_mm9|mouse]]
== FF Samples ==
</td>
{{#ask:[[Category:FF_Samples]][[sample_species::Human (Homo sapiens)]][[is_a::{{FULLPAGENAME}}]]|?name=|format=ul|intro=<h3>Human</h3>}}
  </tr>
{{#ask:[[Category:FF_Samples]][[sample_species::Mouse (Mus musculus)]][[is_a::{{FULLPAGENAME}}]]|?name=|format=ul|intro=<h3>Mouse</h3>}}
{{#ask:[[Category:FF_Samples]][[sample_species::Rat (Rattus rattus)]][[is_a::{{FULLPAGENAME}}]]|?name=|format=ul|intro=<h3>Rat</h3>}}
{{#ask:[[Category:FF_Samples]][[sample_species::Dog (Canis lupus familaris)]][[is_a::{{FULLPAGENAME}}]]|?name=|format=ul|intro=<h3>Dog</h3>}}
{{#ask:[[Category:FF_Samples]][[sample_species::Chicken (Gallus gallus)]][[is_a::{{FULLPAGENAME}}]]|?name=|format=ul|intro=<h3>Chicken</h3>}}


  <tr>
== CAGEd oPOSSUM ==
    <td>'''Sample classifications'''</td>
{{#if:{{{caged_opossum_human|}}}||{{#if:{{{caged_opossum_mouse|}}}||NA}}}}
    <td>
{{#if:{{{caged_opossum_human|}}}|[{{{caged_opossum_human}}} human]{{#if:{{{caged_opossum_mouse|}}}|<br/>|}}|}}
Samples profiled in FANTOM5 are systematically classified by defining FANTON5 sample ontology (FF), consisting of Cell type (CL), Diseases (DOID), and Anatomy (UBERON).
{{#if:{{{caged_opossum_mouse|}}}|[{{{caged_opossum_mouse}}} mouse]|}}
    </td>
    <td> <ul><li>[[CL:0000192|smooth muscle cell]]</li></ul>    </td>
    <td>
[[Cell_Ontology_terms_list|Cell Type (CL)]]


[[Human_Disease_Ontology_terms_list|Disease (DOID)]]
{{#arraymap:{{{namespace}}}|;;|$|{{#set:namespace=$}}}}
{{#arraymap:{{{xref}}}|;;|$|{{#set:xref=$}}}}
{{#arraymap:{{{def}}}|;;|$|{{#set:def=$}}}}
{{#arraymap:{{{is_a}}}|;;|$|{{#set:is_a=$}}}}
{{#arraymap:{{{synonym}}}|;;|$|{{#set:synonym=$}}}}
{{#arraymap:{{{comment}}}|;;|$|{{#set:comment=$}}}}
{{#arraymap:{{{alt_id}}}|;;|$|{{#set:alt_id=$}}}}
{{#arraymap:{{{disjoint_from}}}|;;|$|{{#set:disjoint_from=$}}}}
{{#arraymap:{{{union_of}}}|;;|$|{{#set:union_of=$}}}}
{{#arraymap:{{{created_by}}}|;;|$|{{#set:created_by=$}}}}
{{#arraymap:{{{subset}}}|;;|$|{{#set:subset=$}}}}
{{#arraymap:{{{obo_creation_date}}}|;;|$|{{#set:obo_creation_date=$}}}}
{{#arraymap:{{{adjacent_to}}}|;;|$|{{#set:adjacent_to=$}}}}
{{#arraymap:{{{derives_from}}}|;;|$|{{#set:derives_from=$}}}}
{{#arraymap:{{{develops_from}}}|;;|$|{{#set:develops_from=$}}}}
{{#arraymap:{{{has_quality}}}|;;|$|{{#set:has_quality=$}}}}
{{#arraymap:{{{located_in}}}|;;|$|{{#set:located_in=$}}}}
{{#arraymap:{{{part_of}}}|;;|$|{{#set:part_of=$}}}}


[[Uber_Anatomy_Ontology_terms_list|Anatomy (UBERON)]]
[[Category:FF_Ontology]]
[[Category:FF_Terms]]


[[FF_Ontology_terms_list|FANTOM5 (FF)]]
__NOTOC__
</td>
  </tr>
 
 
 
  <tr>
    <td>'''Co-expression'''</td>
    <td>
CAGE peaks (TSS regions) are grouped based on expression, by using MCL
    </td>
    <td> <ul><li>[[Coexpression_cluster:C18|C18 (in human)]] </li></ul></td>
    <td>
[[Browse_coexpression_clusters|Human]]
 
[[Browse_MCL_coexpression_mouse|Mouse]]
</td>
  </tr>
  <tr>
    <td>'''Motifs'''</td>
    <td>
known and de-novo motifs discovered in the proximal region to the CAGE peaks
    </td>
    <td> <ul><li> [[Novel_motif:1]] </li>  <li> [[JASPAR_motif:MA0002.2|RUNX1]] </li> </ul> </td>
    <td>
<ul>
<li>[[Browse_Novel_motifs|Novel motifs]]</li>
<li>[[Browse_JASPAR_motifs|JASPAR motifs]]</li>
</ul>
</td>
  </tr>
<tr>
    <td>'''Transcription factors'''</td>
    <td>
Transcription factors.
    </td>
    <td> <ul><li>[[EntrezGene:6657|SOX2]]</li></ul>
    </td>
    <td>
[[Browse_Transcription_Factors_hg19|human]]
 
[[Browse_Transcription_Factors_mm9|mouse]]
</td>
  </tr>
 
</table>
<br>
<br>
== Contacts ==
[mailto:fantom-help@gsc.riken.jp?Subject=Fantom5%20WebSite%20Subject&body= help]

Revision as of 16:54, 6 May 2016

outline

  • id: {{{id}}}
  • name: {{{name}}}
  • namespace:
  • def:
  • xref:
  • synonym:
  • comment:
  • alt_id:
  • created_by:
  • subset:
  • creation_date:
  • CAGEd oPOSSUM: NA

Ontology association

Parents

is_a:[[{{{is_a}}}]]()
disjoint_from:[[{{{disjoint_from}}}]]()
union_of:[[{{{union_of}}}]]()
derives_from:[[{{{derives_from}}}]]()
develops_from:[[{{{develops_from}}}]]()
has_quality:[[{{{has_quality}}}]]()
located_in:[[{{{located_in}}}]]()
part_of:[[{{{part_of}}}]]()

Children

FF Samples

CAGEd oPOSSUM

NA








"{{{obo_creation_date}}}" contains an extrinsic dash or other characters that are invalid for a date interpretation.


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