Annotation Extension Relation:has direct input
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) |
note we would not include a separate annotation line for B, because we only have annotation lines for active participants
strictly speaking, the input is SGD:B in the unphosphorylated state and the output is SGD:B in the phosphorylated state. However, currently we do not have IDs for these separate protein forms. Really B is both an input and an output. We standardize on has_input here.
Note there is no need to say:
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(CHEBI:15422 ATP) |
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