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<table>{{#if:{{{name}}}|<tr><th scope="row" align="right" valign="top">[[Property:Name|Name]]:</th><td>[[name::{{{name}}}]]</td></tr>|}}{{#if:{{{namespace}}}|<tr><th scope="row" align="right" valign="top">Namespace:</th><td>{{{namespace}}}</td></tr>|}}{{#if:{{{def}}}|<tr><th scope="row" align="right" valign="top">Definition:</th><td>{{{def}}}</td></tr>|}}{{#if:{{{xref}}}|<tr><th scope="row" align="right" valign="top">Xrefs:</th><td>{{XrefExternalRefs|{{{xref}}}|<br>}}</td></tr>|}}{{#if:{{{synonym}}}|<tr><th scope="row" align="right" valign="top">Synonyms:</th><td>{{CollapsibleOntology|synonym|{{{synonym}}}|;;|<br>}}</td></tr>|}}
{{#if:{{{comment}}}|<tr><th scope="row" align="right" valign="top">Comments:</th><td>{{{comment}}}</td></tr>|}}{{#if:{{{alt_id}}}|<tr><th scope="row" align="right" valign="top">Alt_id:</th><td>{{CollapsibleOntology|alt_id|{{{alt_id}}}|;;|<br>}}</td></tr>|}}{{#if:{{{subset}}}|<tr><th scope="row" align="right" valign="top">Subset:</th><td>{{CollapsibleOntology|subset|{{{subset}}}|;;|<br>}}</td></tr>|}}{{#if:{{{created_by}}}|<tr><th scope="row" align="right" valign="top">Created by:</th><td>{{{created_by}}}</td></tr>|}}{{#if:{{{obo_creation_date}}}|<tr><th scope="row" align="right" valign="top">Creation date:</th><td>{{{obo_creation_date}}}</td></tr>|}}{{#if:{{{has_quality}}}|<tr><th scope="row" align="right" valign="top">Has quality:</th><td>{{{has_quality}}}</td></tr>|}}</table></div>
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== outline ==
*id: [[id::{{{id}}}]]
*name: [[name::{{{name}}}]]
{{#if: {{{namespace}}} | *namespace: {{#show:{{FULLPAGENAME}}|?namespace}}|}}{{#if: {{{def}}} | *def: {{#show:{{FULLPAGENAME}}|?def}}|}}{{#if: {{{xref}}} | *xref: {{#show:{{FULLPAGENAME}}|?xref}}|}}{{#if: {{{is_a}}} | *is_a: {{#arraymap:{{{is_a}}}|;;|$|[[$|{{#show:$|?name}}]]}}|}}{{#if: {{{synonym}}} | *synonym: {{#show:{{FULLPAGENAME}}|?synonym}}|}}{{#if: {{{comment}}} | *comment: {{#show:{{FULLPAGENAME}}|?comment}}|}}{{#if: {{{alt_id}}} | *alt_id: {{#show:{{FULLPAGENAME}}|?alt_id}}|}}{{#if: {{{disjoint_from}}} | *disjoint_from: {{#show:{{FULLPAGENAME}}|?disjoint_from}}|}}{{#if: {{{union_of}}} | *union_of: {{#show:{{FULLPAGENAME}}|?union_of}}|}}{{#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}}|}}{{#if: {{{adjacent_to}}} | *adjacent_to: {{#show:{{FULLPAGENAME}}|?adjacent_to}}|}}{{#if: {{{derives_from}}} | *derives_from: {{#show:{{FULLPAGENAME}}|?derives_from}}|}}{{#if: {{{develops_from}}} | *develops_from: {{#show:{{FULLPAGENAME}}|?develops_from}}|}}{{#if: {{{has_quality}}} | *has_quality: {{#show:{{FULLPAGENAME}}|?has_quality}}|}}{{#if: {{{located_in}}} | *located_in: {{#show:{{FULLPAGENAME}}|?located_in}}|}}{{#if: {{{part_of}}} | *part_of: {{#show:{{FULLPAGENAME}}|?part_of}}|}}
== Children ==
{{#ask:[[is_a::{{FULLPAGENAME}}]]|format=list|intro=*|outro= is_a: {{FULLPAGENAME}}}}{{#ask:[[disjoint_from::{{FULLPAGENAME}}]]|format=list|intro=*|outro= disjoint_from: {{FULLPAGENAME}}}}{{#ask:[[adjacent_to::{{FULLPAGENAME}}]]|format=list|intro=*|outro= adjacent_to: {{FULLPAGENAME}}}}{{#ask:[[derives_from::{{FULLPAGENAME}}]]|format=list|intro=*|outro= derives_from: {{FULLPAGENAME}}}}{{#ask:[[develops_from::{{FULLPAGENAME}}]]|format=list|intro=*|outro= develops_from: {{FULLPAGENAME}}}}{{#ask:[[has_quality::{{FULLPAGENAME}}]]|format=list|intro=*|outro= has_quality: {{FULLPAGENAME}}}}{{#ask:[[located_in::{{FULLPAGENAME}}]]|format=list|intro=*|outro= located_in: {{FULLPAGENAME}}}}{{#ask:[[part_of::{{FULLPAGENAME}}]]|format=list|intro=*|outro= part_of: {{FULLPAGENAME}}}}


== Ontology Tree ==
<onttree nodeid={{{id}}} />


== FF samples ==
{{Fontsize|3|Ontology association}} {{#info:<br>Each term has an is_a parent in the Cell ontology, which has a linkage to an another entity and FANTOM5 samples.Libraries were grouped into mutually exclusive facets according to the FANTOM5 sample ontology mapping to Cell ontologies.
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Human (Homo sapiens)]][[name::+]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Human (Homo sapiens)</b>}}
<br>
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Mouse (Mus musculus)]][[name::+]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Mouse (Mus musculus)</b>}}
<br>link to ontology dataset
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Rat (Rattus rattus)]][[name::+]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Rat (Rattus rattus)</b>}}
<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ff-phase1-prerelease-20130717.obo  data]
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Dog (Canis lupus familaris)]][[name::+]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Dog (Canis lupus familaris)</b>}}
}}
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Chicken (Gallus gallus)]][[name::+]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Chicken (Gallus gallus)</b>}}
----
{{Fontsize|3|Parents}}<br>
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{is_a}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{disjoint_from}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{union_of}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{derives_from}}}|:|0}}|1|0}} +{{#if:{{#pos:{{{has_quality}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{located_in}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{part_of}}}|:|0}}|1|0}} }} |NA|<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>}}
<br><br>
{{Fontsize|3|Children}}
{{#vardefine:is_a_count|{{#ask:[[is_a::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:disjoint_from_count|{{#ask:[[disjoint_from::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:adjacent_to_count|{{#ask:[[adjacent_to::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:derives_from_count|{{#ask:[[derives_from::{{FULLPAGENAME}}]]|format=count}}}}
{{#vardefine:develops_from_count|{{#ask:[[develops_from::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:has_quality_count|{{#ask:[[has_quality::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:located_in_count|{{#ask:[[located_in::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:part_of_count|{{#ask:[[part_of::{{FULLPAGENAME}}]]|format=count}}}}
{{#vardefine:total_element_count|{{#expr:{{#var:is_a_count}}+{{#var:disjoint_from_count}}+{{#var:adjacent_to_count}}+{{#var:derives_from_count}}+{{#var:develops_from_count}}+{{#var:has_quality_count}}+{{#var:located_in_count}}+{{#var:part_of_count}} }} }}{{#ifexpr: {{#var:total_element_count}} > 0 |<table>{{#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>}}</table> |NA}}
== Ontology Tree: Loaded from [http://purl.bioontology.org/ontology/CL BioPortal] ==
{{#ncbo_onttree2:{{#explode:{{{id}}}|:|0}}|{{#explode:{{{id}}}|:|1}}}}
<!--
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<br>
{{Fontsize|3|FF samples}}{{#info:<br>It includes FANTOM5 samples that overlay the [http://cellontology.org/  Cell] ontology.}}
----
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Human (Homo sapiens)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Human (Homo sapiens)</b>}}
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Mouse (Mus musculus)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Mouse (Mus musculus)</b>}}
<!-- {{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Rat (Rattus rattus)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Rat (Rattus rattus)</b>}}
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Dog (Canis lupus familaris)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Dog (Canis lupus familaris)</b>}}
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Chicken (Gallus gallus)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Chicken (Gallus gallus)</b>}} -->


== Enrichment analysis: top 100 FFCP enriched with this ontology term ==
<br>
{{#info:TOP 100 FANTOM5 Cage Peaks enriched with {{{id}}} ({{{name}}}), sorted by p-values <br>Analyst: Hideya Kawaji}}
{{Fontsize|3|Enrichment analysis: top 100 FFCP enriched with this ontology term}}{{#info:TOP 100 FANTOM5 Cage Peaks enriched with {{{id}}} ({{{name}}}), sorted by p-values <br>Analyst: Hideya Kawaji
<br><br>
link to source dataset <br>
human : [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/hg19exp_cell_types_general_term_excluded.txt.gz data]  <br>
mouse : [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/mm9exp_cell_types_general_term_excluded.txt.gz data]
}}
----
{{#ifexpr: {{#ask:[[ffcp_ontology_enrichment_celltype_id::{{{id}}}]]|format=count}} > 0|
{{#ask:[[ffcp_ontology_enrichment_celltype_id::{{{id}}}]]
{{#ask:[[ffcp_ontology_enrichment_celltype_id::{{{id}}}]]
|?ffcp_ontology_enrichment_celltype_p-value|format=template|template=Triplecolumn_to_tbrow|link=none|intro=<html><table class="ont_enrich_ffcp"><thead><tr><th>P-value</th><th>FFCP</th><th>Short description</th></tr></thead><tbody></html>|outro=<html></tbody></table></html>|sort=ffcp_ontology_enrichment_celltype_p-value|order=desc|limit=100|searchlabel=}}
|?ffcp_ontology_enrichment_celltype_p-value|format=template|template=Triplecolumn_to_tbrow|link=none|intro=<html><span id="export_tool"></span><table class="ont_enrich_ffcp stripe cell-border order-column compact"><thead><tr><th>P-value</th><th>FFCP</th><th>Short description</th></tr></thead><tbody></html>|outro=<html></tbody></table></html>|sort=ffcp_ontology_enrichment_celltype_p-value|order=asc|limit=100|searchlabel=}}
|No analysis results for this cluster}}




== Enrichment analysis: top 100 FFCP enriched with this ontology term v019 var. ==
{{#info:TOP 100 FANTOM5 Cage Peaks enriched with {{{id}}} ({{{name}}}), sorted by p-values <br>Analyst: Hideya Kawaji}}
{{#ask:[[ffcp_ontology_enrichment_celltype_v019_id::{{{id}}}]]
|?ffcp_ontology_enrichment_celltype_v019_p-value|format=template|template=Triplecolumn_to_tbrow|link=none|intro=<html><table class="ont_enrich_ffcp"><thead><tr><th>P-value</th><th>FFCP</th><th>Short description</th></tr></thead><tbody></html>|outro=<html></tbody></table></html>|sort=ffcp_ontology_enrichment_celltype_v019_p-value|order=desc|limit=100|searchlabel=}}
<!--
{{#ask:[[ffcp_ontology_enrichment_celltype_id::{{{id}}}]]
|?ffcp_ontology_enrichment_celltype_p-value|format=template|template=Triplecolumn_to_tbrow|link=none|intro=<html><table class="ont_enrich_ffcp"><thead><tr><th>P-value</th><th>FFCP</th><th>Short description</th></tr></thead><tbody></html>|outro=<html></tbody></table></html>|sort=ffcp_ontology_enrichment_celltype_p-value|order=desc|limit=100|searchlabel=}}
-->


{{#arraymap:{{{namespace}}}|;;|$|{{#set:namespace=$}}}}
{{#arraymap:{{{namespace}}}|;;|$|{{#set:namespace=$}}}}
Line 74: Line 127:
{{#arraymap:{{{located_in}}}|;;|$|{{#set:located_in=$}}}}
{{#arraymap:{{{located_in}}}|;;|$|{{#set:located_in=$}}}}
{{#arraymap:{{{part_of}}}|;;|$|{{#set:part_of=$}}}}
{{#arraymap:{{{part_of}}}|;;|$|{{#set:part_of=$}}}}
{{#set:id={{{id}}}}}


[[Category:Cell_Ontology]]
[[Category:Cell_Ontology]]

Latest revision as of 15:17, 13 February 2020

Name:{{{name}}}
Namespace:{{{namespace}}}
Definition:{{{def}}}
Xrefs:
links:
{{{xref}}}:[1]
Synonyms: {{{synonym}}}
Comments:{{{comment}}}
Alt_id: {{{alt_id}}}
Subset: {{{subset}}}
Created by:{{{created_by}}}
Creation date:{{{obo_creation_date}}}
Has quality:{{{has_quality}}}


Ontology association <br>Each term has an is_a parent in the Cell ontology, which has a linkage to an another entity and FANTOM5 samples.Libraries were grouped into mutually exclusive facets according to the FANTOM5 sample ontology mapping to Cell ontologies.<br><br>link to ontology dataset<br>data

Parents
NA

Children


NA

Ontology Tree: Loaded from BioPortal

Ontorolgy tree(Small window open)


FF samples<br>It includes FANTOM5 samples that overlay the Cell ontology.



Enrichment analysis: top 100 FFCP enriched with this ontology termTOP 100 FANTOM5 Cage Peaks enriched with {{{id}}} ({{{name}}}), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

No analysis results for this cluster








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

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