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 | *This relation links two activities when the first activity has a negative regulatory effect on the second activity via a larger process (module) that is reused in many contexts. In this case, curators are not required to model the larger process (module) in every GO-CAM that refers to it. Examples include linking a ubiquitin protein ligase activity to the activity of the protein that is ubiquitinated and degraded. The mechanism is known (in this case, 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 upstream activity to a regulation biological process term (e.g. regulation of proteasome-mediated protein catabolic process has_input target protein) to capture which larger process is left out of the model. | ||
*The 'indirectly | *The 'indirectly negatively 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 (negative) | ||
** Execution of the upstream activity is conditional (regulation) | ** Execution of the upstream activity is conditional (regulation) | ||
== Annotation Usage Guidelines == | == Annotation Usage Guidelines == | ||
*'''What to capture''' | *'''What to capture''' | ||
** This relation is typically used | ** This relation is typically used with upstream activities that are part of activity-regulating biological processes, e.g. negative regulation of gene expression and its children, that reduce expression and thus activity of the downstream target. | ||
*'''What to capture''' | *'''What not 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. | ** 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 == | == 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. | 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. [https://pubmed.ncbi.nlm.nih.gov/24630719/ PMID:24630719] | ||
[[File:Indirect neg.png|500px|Indirectly negatively regulates GO-CAM example]] | |||
* [http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A63d320cd00000182 GO-CAM model] | |||
== Relations Ontology == | == Relations Ontology == | ||
| Line 21: | Line 27: | ||
== Review Status == | == Review Status == | ||
Last reviewed: | Last reviewed: February 15, 2023 | ||
Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Sylvain Poux, Paul Thomas, Kimberly Van Auken | |||
Latest revision as of 13:25, 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 first activity has a negative regulatory effect on the second activity via a larger process (module) that is reused in many contexts. In this case, curators are not required to model the larger process (module) in every GO-CAM that refers to it. Examples include linking a ubiquitin protein ligase activity to the activity of the protein that is ubiquitinated and degraded. The mechanism is known (in this case, 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 upstream activity to a regulation biological process term (e.g. regulation of proteasome-mediated protein catabolic process has_input target protein) to capture which larger process is left out of the model.
- The 'indirectly negatively 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 (negative)
- Execution of the upstream activity is conditional (regulation)
Annotation Usage Guidelines
- What to capture
- This relation is typically used with upstream activities that are part of activity-regulating biological processes, e.g. negative regulation of gene expression and its children, that reduce expression and thus activity of the downstream target.
- What not 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. PMID:24630719
Relations Ontology
indirectly negatively regulates
Review Status
Last reviewed: February 15, 2023
Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Sylvain Poux, Paul Thomas, Kimberly Van Auken