Indirectly positively 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 causal effect in which an upstream activity has a positive (increasing or activating) effect on an downstream activity via at least one intervening activity. The mechanism by which the upstream activity controls the downstream activity should be known. The regulation often leads the execution of an 'activity regulating process'. Activity regulating processes are processes that are constitutive but whose execution is regulated. Examples include transcription, etc.
*This relation is intended to represent a positive causal effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce in this GO-CAM. Examples include linking a transcription factor activity to the activity of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context. In this case, the curator should also include a biological process annotation to GO:xxxxx (regulation of gene expression has_input target gene) to capture which process is left out of the model.


*The 'directly positively regulates' relation is used to relate two GO molecular functions when:
*The 'directly 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 reduces execution of the downstream activity (positive)
** The upstream activity increases 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 12:26, 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 positive causal effect via a larger process (module) that is reused in many contexts, and the curator does not want to reproduce in this GO-CAM. Examples include linking a transcription factor activity to the activity of the transcribed gene. The mechanism is known (transcription and translation) but the process is not specific to this context. In this case, the curator should also include a biological process annotation to GO:xxxxx (regulation of gene expression has_input target gene) to capture which process is left out of the model.
  • The 'directly 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 increases execution of the downstream activity (positive)
    • Execution of the upstream activity is conditional (regulation)

Annotation Usage Guidelines

  • Standard Annotation (TBD - curators could use this to relate MF to MF, but will they want to? Do we need this?)
    • Guidelines
      • What to capture
      • What not to capture
    • Examples
  • GO-CAM
    • 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 increase 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 polymerases, 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 DAF-16 is required for transcription of the cyclin-dependent kinase inhibitor cki-1 in stem cells in response to starvation. In starved daf-16(mgDf50) L1 larvae, physiologically regulated cki-1::GFP expression is absent or diminished in V lineage seam cells, indicating that DAF-16 is required for physiologically regulated expression of cki-1::GFP. In the corresponding GO-CAM model of negative regulation of nematode larval development in response to starvation, DAF-16 thus indirectly positively regulates the cyclin-dependent serine/threonine kinase inhibitor activity of CKI-1.

Relations Ontology

indirectly positively regulates

Review Status

Last reviewed: February 1, 2023


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