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

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m (Annotation Extension Usage Examples)
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'''Targets of protein kinase activity:'''
 
'''Targets of protein kinase activity:'''
  
Statement from paper:
+
Example 1 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).''
 
''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).''
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|  
 
has_direct_input(WB:WBGene00000235 <span style="color:green">baf-1</span>)|has_direct_input(WB:WBGene00017895  <span style="color:green">vrk-1</span>)
 
has_direct_input(WB:WBGene00000235 <span style="color:green">baf-1</span>)|has_direct_input(WB:WBGene00017895  <span style="color:green">vrk-1</span>)
 +
|}
 +
 +
Example 2:
 +
 +
''If protein SGD:A phosphorylates protein SGD:B then annotate A to:''
 +
 +
{| class="wikitable" border="1"
 +
|-
 +
! Gene Name (col 2)
 +
! GO ID (col 5)
 +
! Reference (col 6)
 +
! Evidence (col 7)
 +
! Annotation Extension (col 16)
 +
|-
 +
| SGD:A
 +
|GO:0004672 <span style="color:green">protein kinase activity</span>
 +
| PMID:17170708
 +
| IDA
 +
| has_direct_input(SGD:B <span style="color:green">B</span>)
 
|}
 
|}
  

Revision as of 01:07, 2 June 2014

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

If the entity is indirectly bound/acted upon by the gene product that is the subject of an annotation, then the relation: has_indirect_input should be considered.

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

Annotation Extension Usage Examples

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).

Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
WBGene00000220 GO:0001012 RNA polymerase II regulatory region DNA binding PMID:21502138 IDA

has_direct_input(WB:WBGene00000247 bec-1)|has_direct_input(WB:WBGene00002980 lgg-1)|has_direct_input(WB:WBGene00003033 lin-48)


Targets of protein kinase activity:

Example 1 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).


Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
WBGene00017895 GO:0004672 protein kinase activity PMID:17170708 IDA

has_direct_input(WB:WBGene00000235 baf-1)|has_direct_input(WB:WBGene00017895 vrk-1)

Example 2:

If protein SGD:A phosphorylates protein SGD:B then annotate A to:

Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
SGD:A GO:0004672 protein kinase activity PMID:17170708 IDA has_direct_input(SGD:B B)




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