wiki:RegulationPrinciplesIssuesQuestions

I have folders of notes and e-mails related to regulation. Will try to organise it here: (Note find older regulation document)

  • GO definition "Any process that modulates a measurable attribute of any biological process, quality or function."
    • Is this adequate? What is the definition of modulates? Is it clear that the rate change needs to be *controllable* ? *actively/mechanistically* explicitly controls?
    • Q what is a measureable attribute (frequency, rate or extent?)

Principles

  • To annotate regulation, the gene product must be involved in alteration of the *rate* od a process *in normal cells*
    • i.e. a mutant changing the rate of a process occurance alone does not consitute regulation
  • regulation can be upstream or within a process or pathway
    • Whether something is upstream regulation depends on where the start of the pathway is defined

Questions

  • Is regulation of an activity subtly different from "regulation of a process" and if so, how are they related?
  • Are there any "regulation of" which are not annotated to signal transduction? if not could they be, and if still not, what are they?
  • Regulation within a process always involves altering a specific gene product enzyme/activity in a pathway.
    • How can this be achieved?
      • Allostery
      • How does regulation of localisation fit in? Is the entity which does the localising necessarily the regulator? does the actual regulation happen upstream? which gene in the localizationpathway are the regulator(s)? all of them?

  • Q: Can a term have regulation and part_of relation to a single parent simultaneously ? Q: Is it ever part_of a different process?
  • Q: When is upstream regulation not signal transduction?

Things to look at

  • The GO slim number s between involved in and regulates are getting very close…assess differences

Related SF tickets

Consequences for searching and filtering

  • Follow up transitivity over regulation raised at last GO meeting
Last modified 7 years ago Last modified on Jan 23, 2014, 10:18:02 AM