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necessary & sufficient

David Sutherland djs93 at gen.cam.ac.uk
Mon Feb 16 03:52:46 PST 2004


Hi Stan,

I'm not party to any GO discussions of defintitions for these
terms, but here's by penneth anyway:

If a loss of function mutation results in a phenotype in which a structure
or function is absent, than that gene can be considered necessary for that
function/structure.
- the 2 problems I can see with this are:
1. what to do in situations when penetrance or expressivity of the
phenotype is low (& environmental effects on these)
2. How to account for genetic background - it is always feasible that some
genetic background exists in which loss of function mutations of the gene
do not cause loss of the structure/function.  Perhaps the way sround this
is to always express necessary with a tag giving genetic background - the
default being that mythical beast 'wild-type'.

The geneticist/developmental biologist definition of sufficient, as I see
it: If overexpression of a gene results in formation of an ectopic
structure or function (even at low levels of penetrance or expressivity) 
then it is sufficient for formation of that structure/funtion.  Again, I
think genetic and environmental background need to be recorded (with
default as WT).

A more ambiguous situation is in the case of overexpression of activated
forms (e.g.- activated receptors).  Excluding these would avoid some
difficult calls: 1.  does the activation strictly mimic activation of
'normal' physiological function ?
2. How do we deal with spontaneous mutations leading to activation of a
function (not uncommon with receptors)?


Note: There is also a competing use of the term sufficient by computer
modellers, whose aim is often to find the minimal set of components and
parameters "sufficient" for a system (e.g.- mechanism for patterning of
some structure) to produce the same output as the system being studied.

Hope this is useful,

David 


David Sutherland
FlyBase, Cambridge UK


On Sat, 14 Feb 2004 SLetovsky at aol.com wrote:

> Gofriends,
> 
>     Does anyone know of any attempts to define necessary and sufficient 
> criteria
> for GO associations? I am familiar with the attempts to provide rigorous 
> semantics
> for ISA and partof, but I have not seen anything comparable for determining 
> when it is
> correct to say that a term does or does not apply to a gene or protein -- 
> e.g. what
> experimental result would suffice to answer the question. 
> 
> Cheers, -Stan
> 


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