Removes input for: Difference between revisions

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== Overview and Scope of Use ==
== Overview and Scope of Use ==
*This relation is used in GO-CAMs but not in standard annotation extensions.
*This relation is used in GO-CAMs but not in standard annotation extensions.
* This relation is intended to represent a negative causal effect of an upstream activity on a downstream activity, in which the two activities act on or modify the same molecular target at the same site(s). As a result, the execution of the upstream activity prevents the downstream activity from occurring (or reduces its rate). This acts like in a molecular 'switch' between two outcomes.
* This relation links two activities when the upstream activity effects the execution of the downstream activity due to the two activities acting on or modifying the same molecular target at the same site(s). As a result, the execution of the upstream activity prevents the downstream activity from occurring (or reduces its rate). This acts like a molecular 'switch' between two outcomes.
*The 'removes input for' relation is used to relate GO Molecular Functions (MF) when:
*The 'removes input for' relation is used to relate GO Molecular Functions (MF) when:
**The upstream MF occurs before the downstream MF
**The upstream activity occurs before the downstream activity
**The upstream MF has a negative effect on the downstream MF
**The upstream activity has a negative effect on the downstream activity
**The execution of the upstream MF results in an input of the downstream MF becoming unavailable for the downstream MF
**The execution of the upstream activity results in an input of the downstream activity becoming unavailable for the downstream activity


== Annotation Usage Guidelines ==
== Annotation Usage Guidelines ==
* '''What to capture'''
* '''What to capture'''
** This relation should be used to capture processes where the cell or organism has a 'choice' about a causal pathway and one choice excludes the other because a substrate is no loger available for a step in the other pathway. Two examples of this are the 'histone code' (PMID:11498575) and the 'ubiquitin code' (PMID:27012465), in which a modification of an amino acid essentially makes that amino acid unavailable for a different modification.
** This relation should be used to capture processes where the cell or organism has a 'choice' about a causal pathway and one choice excludes the other because a substrate is no longer available for a step in the other pathway. Two examples of this are the 'histone code' ([https://pubmed.ncbi.nlm.nih.gov/11498575/ PMID:11498575)] and the 'ubiquitin code' [https://pubmed.ncbi.nlm.nih.gov/27012465/ (PMID:27012465)], in which a modification of an amino acid makes that amino acid unavailable for a different modification.
* '''What not to capture'''
* '''What not to capture'''
** This relation should not be used for inducible activities that remove substrates or inputs of a downstream activity in order to regulate the process.
** This relation should not be used for inducible activities that remove substrates or inputs of a downstream activity in order to regulate the process.


==Examples==
==Examples==
* Methylation of CpG islands in promoters and enhancers prevents DNA binding transcription factors from being able to interact with those regions. So although the overall process is regulatory, the activity of the methyltransferase removes an input (the promoter region or enhancer region) for the DNA binding transcription factor.  
* Methylation of CpG islands in promoters and enhancers prevents DNA binding transcription factors from being able to interact with those regions. So although the overall process is regulatory, the activity of the methyltransferase removes an input (the promoter region or enhancer region) for the DNA binding transcription factor. [https://pubmed.ncbi.nlm.nih.gov/36471082/ PMID:36471082]


[[File:Removes_input.png|500px|Removes input for GO-CAM example]]
[[File:Removes_input.png|500px|Removes input for GO-CAM example 1]]
Removes_input


[http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A63894f2500000608 Link to GO-CAM model]
[http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A63894f2500000608 GO-CAM model]
 
* KMT5A methylates histones H4 at Lys-20, preventing the histone reader activity of TONSL, which specifically binds histone H4 lacking methylation at 'Lys-20' (H4K20me0). [https://pubmed.ncbi.nlm.nih.gov/27338793/ PMID:27338793]
[[File:Removes_input-2.png|500px|Removes input for GO-CAM example 2]]
 
[http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A623d156d00000817 GO-CAM model]


== Ontology Usage Guidelines ==
== Ontology Usage Guidelines ==
Line 28: Line 33:


== Review Status ==
== Review Status ==
Modified on October 31, 2022
Last reviewed: February 15, 2023
 
Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Chris Mungall, Paul Thomas, Kimberly Van Auken
 


Last reviewed:


[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]
[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]

Latest revision as of 10:25, 16 March 2023

Overview and Scope of Use

  • This relation is used in GO-CAMs but not in standard annotation extensions.
  • This relation links two activities when the upstream activity effects the execution of the downstream activity due to the two activities acting on or modifying the same molecular target at the same site(s). As a result, the execution of the upstream activity prevents the downstream activity from occurring (or reduces its rate). This acts like a molecular 'switch' between two outcomes.
  • The 'removes input for' relation is used to relate GO Molecular Functions (MF) when:
    • The upstream activity occurs before the downstream activity
    • The upstream activity has a negative effect on the downstream activity
    • The execution of the upstream activity results in an input of the downstream activity becoming unavailable for the downstream activity

Annotation Usage Guidelines

  • What to capture
    • This relation should be used to capture processes where the cell or organism has a 'choice' about a causal pathway and one choice excludes the other because a substrate is no longer available for a step in the other pathway. Two examples of this are the 'histone code' (PMID:11498575) and the 'ubiquitin code' (PMID:27012465), in which a modification of an amino acid makes that amino acid unavailable for a different modification.
  • What not to capture
    • This relation should not be used for inducible activities that remove substrates or inputs of a downstream activity in order to regulate the process.

Examples

  • Methylation of CpG islands in promoters and enhancers prevents DNA binding transcription factors from being able to interact with those regions. So although the overall process is regulatory, the activity of the methyltransferase removes an input (the promoter region or enhancer region) for the DNA binding transcription factor. PMID:36471082

Removes input for GO-CAM example 1

GO-CAM model

  • KMT5A methylates histones H4 at Lys-20, preventing the histone reader activity of TONSL, which specifically binds histone H4 lacking methylation at 'Lys-20' (H4K20me0). PMID:27338793

Removes input for GO-CAM example 2

GO-CAM model

Ontology Usage Guidelines

This relation is not used in the ontology.

Relations Ontology

removes input for

Review Status

Last reviewed: February 15, 2023

Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Chris Mungall, Paul Thomas, Kimberly Van Auken


Back to: Annotation Relations