Annotation Extension Relation:has regulation target: Difference between revisions

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Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation  Annotation usage examples for each annotation extension relation]
#REDIRECT [[Annotation]]
 
'''USAGE OF THIS RELATION HAS BEEN DEPRECATED'''
 
<pre style="color:#808080">
 


==Definition==
==Definition==


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


==Child terms==
==Child terms==
Line 26: Line 32:


''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).''   
''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




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| PMID:21502138
| PMID:21502138
| IMP
| 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>
has_regulation_target(WB:WBGene00000247 <span style="color:green">bec-1</span>)|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 ====
==== Specifying the gene which is a target of a transcription factor ====


'''gene transcription targets'''  <span style="color:red">'''This example is still under discussion.''' </span>
'''gene transcription targets'''   


Statement example:  
Statement example:  


''DNA binding transcription factor A binds the promoter of Polo2 and increases transcription of Polo2''
''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"
{| class="wikitable" border="1"
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|-
|-
| Unfolded
| Unfolded
| Pxxx <span style="color:green">transcription factor A</span>
| WBGene00000220 <span style="color:green">atf-2(tm467)</span>
| GO:0001228 <span style="color:green">RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription</span>
| GO:0000122 <span style="color:green">negative regulation of transcription from RNA polymerase II promoter</span>
| PMID:xxx
| PMID:21502138
| IDA
| IMP
| has_regulation_target(UNIPROT:Qxxx <span style="color:green">Polo2</span>)
| 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]
</pre>
 
 
----
 
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:Deprecated]]
[[Category:annotation extension]]

Latest revision as of 08:37, 27 September 2021

Redirect to:

USAGE OF THIS RELATION HAS BEEN DEPRECATED

 


==Definition==

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


==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


{| 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>