Annotation Extension Relation:has regulation target: Difference between revisions

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==Definition==
==Definition==


Identifies a gene or gene product affected by a regulation BP (or regulator MF).
Identifies a gene or gene product affected by a regulation Biological Process or regulator Molecular Function.
 
==Comment==
 
[http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_participant#Comment '''More details on the limited use of has_regulation_target with regulation of biological process annotations''']


==Child terms==
==Child terms==


* None
* None
==Scope of use==
===Domain===
GO:0065007 ! biological regulation
===Range===
[[ENTITY_UNION:0000005]] ! chemical, gene product or complex


==Annotation Extension Usage Examples==
==Annotation Extension Usage Examples==
'''Loss of transcription factor activity affects gene expression:'''
Statements from paper: 
''Indeed, LGG-1 was massively upregulated in atf-2(tm467) mutant embryos, as compared with the wild type (Fig. 6A). We observed a similar extent of BEC-1 upregulation in the atf-2-deficient background (data not shown).'' 
Expressed in LEGO: http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_6239-548253760000031
{| class="wikitable" border="1"
|-
! Gene Name (col 2)
! GO ID (col 5)
! Reference (col 6)
! Evidence (col 7)
! Annotation Extension (col 16)
|-
| WBGene00000220 atf-2(tm467)
|GO:0000122 <span style="color:green">negative regulation of transcription from RNA polymerase II promoter</span>
| PMID:21502138
| IMP
| has_regulation_target(WB:WBGene00000247 <span style="color:green">bec-1</span>) 'pipe' has_regulation_target(WB:WBGene00002980 <span style="color:green">lgg-1</span>
|}
== Using examples (from above) to demonstrate [[Folding_and_Unfolding]] using the relationship has_regulation_target ==
==== Specifying the gene which is a target of a transcription factor ====
'''gene transcription targets''' 
Statement example:
''Indeed, LGG-1 was massively upregulated in atf-2(tm467) mutant embryos, as compared with the wild type (Fig. 6A). We observed a similar extent of BEC-1 upregulation in the atf-2-deficient background (data not shown).''
{| class="wikitable" border="1"
|-
! Folded/unfolded
! Gene Name (col 2)
! GO ID (col 5)
! Reference (col 6)
! Evidence (col 7)
! Annotation Extension (col 16)
! Parent terms of new folded GO term
|-
| Unfolded
| WBGene00000220 <span style="color:green">atf-2(tm467)</span>
| GO:0000122 <span style="color:green">negative regulation of transcription from RNA polymerase II promoter</span>
| PMID:21502138
| IMP
| has_regulation_target(WB:WBGene00000247 <span style="color:green">bec-1</span>)'pipe' has_regulation_target(WB:WBGene00002980 <span style="color:green">lgg-1</span>
|-
| Folded
| WBGene00000220 <span style="color:green">atf-2(tm467)</span>
| GO:0000122 <span style="color:green">negative regulation of transcription from RNA polymerase II promoter</span>
| PMID:21502138
| IMP
|
| <span style="color:red">No new GO term created</span>
|-
|}
'''OWL class expression:''' GO:0000122 <span style="color:red">negative regulation of transcription from RNA polymerase II promoter</span> AND has_regulation_target SOME WB:WBGene00000247 <span style="color:red">bec-1</span>
'''OWL class expression:''' GO:0000122 <span style="color:red">negative regulation of transcription from RNA polymerase II promoter</span> AND has_regulation_target SOME WB:WBGene00002980 <span style="color:red">lgg-1</span>
Back to [http://wiki.geneontology.org/index.php/Annotation_Extension:_Capturing_participants Annotation Extension: Capturing participants]
----
Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation  Annotation usage examples for each annotation extension relation]
[[Category:relations]]
[[Category:annotation extension]]

Revision as of 08:44, 8 May 2015

Back to Annotation usage examples for each annotation extension relation

Definition

Identifies a gene or gene product affected by a regulation Biological Process or regulator Molecular Function.

Comment

More details on the limited use of has_regulation_target with regulation of biological process annotations

Child terms

  • None

Scope of use

Domain

GO:0065007 ! biological regulation

Range

ENTITY_UNION:0000005 ! chemical, gene product or complex

Annotation Extension Usage Examples

Loss of transcription factor activity affects gene expression:

Statements from paper:

Indeed, LGG-1 was massively upregulated in atf-2(tm467) mutant embryos, as compared with the wild type (Fig. 6A). We observed a similar extent of BEC-1 upregulation in the atf-2-deficient background (data not shown).

Expressed in LEGO: http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_6239-548253760000031


Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
WBGene00000220 atf-2(tm467) GO:0000122 negative regulation of transcription from RNA polymerase II promoter PMID:21502138 IMP has_regulation_target(WB:WBGene00000247 bec-1) 'pipe' has_regulation_target(WB:WBGene00002980 lgg-1

Using examples (from above) to demonstrate Folding_and_Unfolding using the relationship has_regulation_target

Specifying the gene which is a target of a transcription factor

gene transcription targets

Statement example:

Indeed, LGG-1 was massively upregulated in atf-2(tm467) mutant embryos, as compared with the wild type (Fig. 6A). We observed a similar extent of BEC-1 upregulation in the atf-2-deficient background (data not shown).

Folded/unfolded Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16) Parent terms of new folded GO term
Unfolded WBGene00000220 atf-2(tm467) GO:0000122 negative regulation of transcription from RNA polymerase II promoter PMID:21502138 IMP has_regulation_target(WB:WBGene00000247 bec-1)'pipe' has_regulation_target(WB:WBGene00002980 lgg-1
Folded WBGene00000220 atf-2(tm467) GO:0000122 negative regulation of transcription from RNA polymerase II promoter PMID:21502138 IMP No new GO term created

OWL class expression: GO:0000122 negative regulation of transcription from RNA polymerase II promoter AND has_regulation_target SOME WB:WBGene00000247 bec-1 OWL class expression: GO:0000122 negative regulation of transcription from RNA polymerase II promoter AND has_regulation_target SOME WB:WBGene00002980 lgg-1


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