Indirectly positively regulates: Difference between revisions

Revision as of 12:50, 7 February 2023

This relation is used in GO-CAMs but not in standard annotation extensions.
This relation is intended to represent a positive 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 transcription factor activity to the activity of the product of the transcribed gene. The mechanism is known (transcription and translation) 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 gene expression has_input target gene) 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 increases execution of the downstream activity (positive)
- Execution of the upstream activity is conditional (regulation)

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 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.

Last reviewed: February 7, 2023

Reviewed by: Cristina Casals, Marc Feuermann, Pascale Gaudet, David Hill, Patrick Masson, Sylvain Poux, Paul Thomas, Kimberly Van Auken

@@ Line 13: / Line 13: @@
 ** 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.
+** 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 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.