Indirectly negatively regulates: 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 | *This relation is intended to represent a negative regulatory effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. Examples include linking a ubiquitin protein ligase activity (the specificity factor) to the activity of the protein that is ubiquitinated and degraded. The mechanism is known (proteasome-mediated protein degradation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the activity to GO:xxxxx (regulation of proteasome-mediated protein catabolic process has_input target protein) to capture which process is left out of the model. | ||
*The 'indirectly positively regulates' relation is used to relate two GO molecular functions when: | *The 'indirectly positively regulates' relation is used to relate two GO molecular functions when: | ||
** The upstream activity occurs before the downstream activity, but there are intervening activities between them (indirect) | ** The upstream activity occurs before the downstream activity, but there are intervening activities between them (indirect) | ||
** The mechanism that relates the upstream activity to the downstream activity is understood | ** The mechanism that relates the upstream activity to the downstream activity is understood | ||
** The upstream activity | ** The upstream activity decreases execution of the downstream activity (positive) | ||
** Execution of the upstream activity is conditional (regulation) | ** Execution of the upstream activity is conditional (regulation) | ||
Revision as of 12:49, 7 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 regulatory effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce that module in this GO-CAM. Examples include linking a ubiquitin protein ligase activity (the specificity factor) to the activity of the protein that is ubiquitinated and degraded. The mechanism is known (proteasome-mediated protein degradation) but the process is not specific to this context, and would not be included in the model. In this case, the curator should also include a part_of link from the activity to GO:xxxxx (regulation of proteasome-mediated protein catabolic process has_input target protein) to capture which process is left out of the model.
- The 'indirectly positively regulates' relation is used to relate two GO molecular functions when:
- The upstream activity occurs before the downstream activity, but there are intervening activities between them (indirect)
- The mechanism that relates the upstream activity to the downstream activity is understood
- The upstream activity decreases execution of the downstream activity (positive)
- Execution of the upstream activity is conditional (regulation)
Annotation Usage Guidelines
- What to capture
- This relation is typically used for MFs that are part of activity-regulating BPs, e.g. regulation of gene expression and its children, that reduce expression and thus, activity, of the downstream target.
- What to capture
- Indirectness indicates that there are intervening activities, e.g. general transcription factor activities or endoribonucleases, between the two activities connected with this relation. Since the intervening activities may be part of a larger coordinated process of gene expression, it is not necessary for curators to model the entire coordinated process in their GO-CAM.
Example
C. elegans msi-1 encodes a member of the Musashi family of RNA-binding proteins that, in response to signaling via an AMPA-type glutamate receptor, binds to mRNA 3'UTRs encoding members of the Arp2/3 complex to repress their translation and alter actin cytoskeleton organization in the context of regulation of memory loss. In a GO-CAM, this indirect regulation is modeled as: mRNA base-pairing translational repressor activity enabled by MSI-1 indirectly negatively regulates actin binding activity enabled by ARX-2.
Relations Ontology
indirectly negatively regulates
Review Status
Last reviewed: January 31, 2023