Indirectly negatively regulates: Difference between revisions

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** Guidelines
** Guidelines
*** What to capture
*** 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.
**** 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 not to capture
*** What not to capture
**** This relation should not be used to capture upstream activities that occur before a downstream activity, but aren't necessary for the downstream activity to occur.
**** 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.
** Examples
** Example
*** PDI-6 encodes a protein disulfide isomerase that is required for proper folding of the receptor EGL-20. We understand what PDI-6 does, it is constitutive and if its activity is absent, EGL-20 is misfolded, degraded and cannot function. [https://pubmed.ncbi.nlm.nih.gov/35675782/ Link to reference]
***
**** [http://noctua.geneontology.org/editor/graph/gomodel:5b91dbd100001628 EGL-20 maturation - constitutively upstream of]
*** Zdhhc9 post-translationally modifies Nras with a palmitoyl group, resulting in its membrane association. The membrane association of an oncogenic form of NRAS that has low GTPase activity is required for its oncogenic (signaling) activity. Inhibiting the activity of Zdhhc9 decreases palmitoylation and the biological activity of oncogenic Nras. [https://pubmed.ncbi.nlm.nih.gov/26493479/ Link to reference]
**** [http://noctua.geneontology.org/editor/graph/gomodel:635b1e3e00001677?model_id=gomodel:635b1e3e00001677 constitutively upstream of example 2]


== Quality Control Checks ==
== Quality Control Checks ==

Revision as of 10:43, 26 January 2023

Overview and Scope of Use

  • The 'indirectly negatively regulates' relation is used to relate GO Molecular Functions (MF) 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 reduces execution of the downstream activity (negative)
    • 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 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

Quality Control Checks

  • Annotations can be validated using a Shape Expressions (ShEx) representation of allowed relations between ontology terms.

Child Terms

Relations Ontology

constitutively upstream of

Review Status

Last reviewed: October 31, 2022


Back to: Annotation Relations