Removes input for: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
Line 20: Line 20:


[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 Link to GO-CAM model]
* Modification of histones affect the ability of histone readers to recognize them, and affect transcription.


== Ontology Usage Guidelines ==
== Ontology Usage Guidelines ==

Revision as of 10:05, 8 February 2023

Overview and Scope of Use

  • 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.
  • The 'removes input for' relation is used to relate GO Molecular Functions (MF) when:
    • The upstream MF occurs before the downstream MF
    • The upstream MF has a negative effect on the downstream MF
    • The execution of the upstream MF results in an input of the downstream MF becoming unavailable for the downstream MF

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 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.
  • 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.

Removes input for GO-CAM example Removes_input

Link to GO-CAM model

  • Modification of histones affect the ability of histone readers to recognize them, and affect transcription.

Ontology Usage Guidelines

This relation is not used in the ontology.

Relations Ontology

removes input for

Review Status

Modified on October 31, 2022

Last reviewed:

Back to: Annotation Relations