Indirectly positively regulates: Difference between revisions

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** Example
** 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.
*** 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.
== Quality Control Checks ==
* Annotations can be validated using a Shape Expressions ([https://github.com/geneontology/go-shapes/blob/master/shapes/go-cam-shapes.shex ShEx]) representation of allowed relations between ontology terms.
== Child Terms ==


== Relations Ontology ==
== Relations Ontology ==

Revision as of 10:39, 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 causal effect in which an upstream activity has a positive (increasing or activating) effect on an downstream activity via at least one intervening activity that is often part of an 'activity regulating process'. Activity regulating processes are processes that are constitutive but whose execution is regulated. Examples include transcription, proteasome-mediated degradation, etc.


Immediately means there is no activity. The mechanism by which the upstream activity controls the downstream activity should be known. The regulation commonly involves direct physical interaction between the two enablers, but may also occur when the upstream activity produces or degrades a small molecule regulator of the downstream activity. The 'directly positively regulates' relation is commonly used between successive functions in a regulatory pathway, such as a signaling pathway.

  • The 'directly positively regulates' relation is used to relate two GO molecular functions when:
    • Two molecular functions act in direct succession (i.e. there is no intervening molecular function)
    • The upstream molecular function exerts its regulation on the downstream function by a direct effect on the enabler of the downstream function
    • The direct effect on the enabler enhances its ability to execute its function

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


Back to: Annotation Relations