Difference between revisions of "Annotation Extension Relation:has direct input"

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'''THIS RELATION IS DEPRECATED'''
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Curators should use  [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_input has input] to capture inputs/substrates/targets of Molecular Functions
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<pre style="color:#808080">
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==Definition==
 
==Definition==
  
 
Identifies an entity directly affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in a Molecular Function or Biological Process.
 
Identifies an entity directly affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in a Molecular Function or Biological Process.
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==Comment==
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To use this relationship there must be evidence that the gene product in column 2 is known/predicted to bind the molecular target in column 16.
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This can be a co-immunoprecipitation (for example) demonstrated in the paper being annotated, or from evidence available in another paper, or from evidence of protein interactions which have been demonstrated in another paper for orthologous molecules.
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Without evidence of a relevant interaction use the relationship has_input
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==Synonyms==
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directly_localizes (NARROW)
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has_direct_target (EXACT)
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has_substrate (NARROW)
  
 
==Child terms==
 
==Child terms==
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[[ENTITY_UNION:0000005]] ! chemical, gene product, or complex
 
[[ENTITY_UNION:0000005]] ! chemical, gene product, or complex
  
==Annotation Extension Usage Examples==
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</pre>
 
 
'''Transcription factor binding to potential target sequences in vitro:'''
 
 
 
Statement from paper: 
 
 
 
''By performing gel electrophoretic mobility shift assays, we could detect efficient binding of ATF-2 to the elements found in the bec-1 and lgg-1 promoters (Fig. 5C).'' 
 
 
 
(Note that binding to lin-48 is also reported as a positive control).
 
 
 
{| class="wikitable" border="1"
 
|-
 
! Gene Name (col 2)
 
! GO ID (col 5)
 
! Reference (col 6)
 
! Evidence (col 7)
 
! Annotation Extension (col 16)
 
|-
 
| WBGene00000220
 
|GO:0001012 <span style="color:green">RNA polymerase II regulatory region DNA binding</span>
 
| PMID:21502138
 
| IDA
 
|
 
has_direct_input(WB:WBGene00000247 <span style="color:green">bec-1</span>)|has_direct_input(WB:WBGene00002980 <span style="color:green">lgg-1</span>)|has_direct_input(WB:WBGene00003033 <span style="color:green">lin-48</span>)
 
 
 
|}
 
 
 
 
 
'''Targets of protein kinase activity:'''
 
 
 
Statement from paper:
 
 
 
''A final line of evidence that BAF-1 is a substrate for VRK-1 was obtained with purified recombinant proteins, which demonstrated that BAF-1 was phosphorylated by VRK-1 in vitro (Figure 4H, lower panel). In addition, VRK-1 was autophosphorylated (Figure 4H, upper panel).''
 
 
 
 
 
{| class="wikitable" border="1"
 
|-
 
! Gene Name (col 2)
 
! GO ID (col 5)
 
! Reference (col 6)
 
! Evidence (col 7)
 
! Annotation Extension (col 16)
 
|-
 
| WBGene00017895
 
|GO:0004672 <span style="color:green">protein kinase activity</span>
 
| PMID:17170708
 
| IDA
 
|
 
has_direct_input(WB:WBGene00000235 <span style="color:green">baf-1</span>)|has_direct_input(WB:WBGene00017895  <span style="color:green">vrk-1</span>)
 
|}
 
 
 
 
 
----
 
  
  

Latest revision as of 13:57, 20 January 2020

THIS RELATION IS DEPRECATED

Curators should use has input to capture inputs/substrates/targets of Molecular Functions

 

==Definition==

Identifies an entity directly affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in a Molecular Function or Biological Process.

==Comment==
To use this relationship there must be evidence that the gene product in column 2 is known/predicted to bind the molecular target in column 16.
 
This can be a co-immunoprecipitation (for example) demonstrated in the paper being annotated, or from evidence available in another paper, or from evidence of protein interactions which have been demonstrated in another paper for orthologous molecules.

Without evidence of a relevant interaction use the relationship has_input

==Synonyms==

directly_localizes (NARROW)

has_direct_target (EXACT)

has_substrate (NARROW)

==Child terms==

* None

==Scope of use==

===Domain===

BFO:0000007 ! process (Biological Process or Molecular Function) 

===Range===

[[ENTITY_UNION:0000005]] ! chemical, gene product, or complex


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Back to Annotation usage examples for each annotation extension relation