Has input: Difference between revisions

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Line 190: Line 190:
| Pxxx <span style="color:green">transcription factor A</span>
| Pxxx <span style="color:green">transcription factor A</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: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>
| PMID:xxx
| IDA
|
| <span style="color:red">No new GO term created</span>
|-
| Unfolded
| Pxxx <span style="color:green">transcription factor A</span>
| GO:0044212 <span style="color:green">transcription regulatory region DNA binding</span>
| PMID:xxx
| IDA
| has_direct_target(UNIPROT:Qxxx <span style="color:green">Polo2</span>)
|
|-
| Folded
| Pxxx <span style="color:green">transcription factor A</span>
| GO:0044212 <span style="color:green">transcription regulatory region DNA binding</span>
| PMID:xxx  
| PMID:xxx  
| IDA
| IDA

Revision as of 11:58, 16 June 2014

Back to Annotation usage examples for each annotation extension relation

Definition

Identifies an entity affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in a molecular function or biological process.

Synonyms

has_target (EXACT)

localizes (NARROW)

Child terms

If you know that the target is bound by the annotated gene product then consider using this child relationship

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

Enhancing Molecular Function and Biological Process Annotations

Specifying the chemical that was applied and induced a 'response to chemicals'

I think that in_presence_of might be a better relationship choice, but left the example here awaiting confirmation (Ruth)

Here we use the has_input relation - the input to the process is a chemical, the output is some change in state as a result of exposure.

 col5: GO:nnnnnn
 col16: has_input(CHEBI:nnnnn)

Sometimes it is better to request a GO term here


Cellular response to drug

Statement from paper: incubation of cells with low concentrations of phenformin and depletion of Ppm1E increased AMPK phosphorylation

So one of the annotations would be:


DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Evidence (Col 7) Extension (Col 16)
Q8WY54 PPM1E GO:0035690 cellular response to drug PMID:20801214 IDA has_input(CHEBI:6801 metformin)

Specifying the protein which is a target of a Biological Process

Proteolysis targets

Statement from paper: MICA shedding by tumor cells was inhibited by silencing of the related ADAM10 and ADAM17 proteases

So one of the annotations would be:

DB (Col 2) Object (Col 3) GO ID (Col 5) Reference (Col 6) Evidence (Col 7) Extension (Col 16)
O14672 ADAM10 GO:0006509 membrane protein ectodomain proteolysis PMID:18676862 IMP has_input(UNIPROT:Q29983 MICA)

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

Specifying the protein which is a target of a Biological Process

Proteolysis targets

Statement from paper: MICA shedding by tumor cells was inhibited by silencing of the related ADAM10 and ADAM17 proteases

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 O14672 ADAM10 GO:0006509 membrane protein ectodomain proteolysis PMID:18676862 IMP has_input(UNIPROT:Q29983 MICA)
Folded O14672 ADAM10 GO:0006509 membrane protein ectodomain proteolysis PMID:18676862 IMP No new GO term created

No new term will be created in this example because this is outside of the scope of GO, although tools using GO could use the relationship to create the following:

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 O14672 ADAM10 GO:0006509 membrane protein ectodomain proteolysis PMID:18676862 IMP has_input(UNIPROT:Q29983 MICA)
Folded O14672 ADAM10 New GO term membrane protein ectodomain proteolysis of MICA PMID:18676862 IMP GO:0006509 membrane protein ectodomain proteolysis

Specifying the gene which is a target of a transcription factor

gene transcription targets

Statement example:

DNA binding transcription factor A binds the promoter of Polo2 and increases transcription of Polo2

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 Pxxx transcription factor A GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription PMID:xxx IDA has_direct_regulation target(UNIPROT:Qxxx Polo2)
Folded Pxxx transcription factor A GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription PMID:xxx IDA No new GO term created
Unfolded Pxxx transcription factor A GO:0044212 transcription regulatory region DNA binding PMID:xxx IDA has_direct_target(UNIPROT:Qxxx Polo2)
Folded Pxxx transcription factor A GO:0044212 transcription regulatory region DNA binding PMID:xxx IDA No new GO term created

No new term will be created in this example because this is outside of the scope of GO, although tools using GO could use the relationship to create the following:

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 Pxxx transcription factor A New GO term RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription PMID:xxx IDA has_input(UNIPROT:Qxxx Polo2)
Folded Pxxx transcription factor A GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription of Polo2 PMID:xxx IDA GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription



Back to Annotation usage examples for each annotation extension relation