Has input: Difference between revisions
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| 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