[go] contributes_to question

[Midori Harris]

Whatever we decide, I would recommend that computational analyses omit 
'contributes_to' annotations.

m

On Mon, 13 Aug 2007, Valerie Wood wrote:

> Recently I'm wondering recently why we have 2 meanings for contributes_to:
>
> When the qualifier was initially implemented, it was so function terms could 
> be added to complexes like DNA polymerase and the F1 Fo ATPase where the 
> function cannot be attributed to a single subunit. This seems fine.
>
> Increasingly I see annotations to complexes which are described as (for 
> example) a histone acetyltransferase complex, and all of the subunits are 
> given histone de/acetlytransferase or methyltransferase activity with 
> contributes_to, even thought the other subunits clearly have other functions 
> (I see ATPases, ubiquitin ligases actin-like proteins etc, which are commonly 
> associated with histone acetyltransferases and methyltransferases).
>
> This seems odd, for a number of reasons.
> Often these subunits are not required for the activity, but their deletion 
> (sometimes, but not always) affects the rate  the activity
>
> Primarily I don't understand what this type of 'contributes_to' annotation 
> provides  to GO users above a process annotation to the histone acetylation 
> (if this has been shown), a complex annotation, and a function term to 
> unknown/root node.  Isn't it more useful to know that there is some 
> information about the process, but the molecular function is not known?
>
> 1) Another problem is that these particular chromatin associated complexes 
> often have shared subunits so the function annotations aren't so clear-cut 
> (i.e some of these subunits may be members of other complexes which do not 
> have this activity)
>
> 2) Also computational analysis using RCA which infer these 'functions' to 
> similar proteins which, from their domain composition it is unlikely possess 
> this activity. 
> 3) It makes cross species comparisons difficult because you get different 
> numbers of functions to what you would  expect when comparing annotations 
> between species. For example it is known how many histone acetyltransferases 
> /methytrasferases etc. pombe has, compered to S. cerevisiae, but when I 
> compare the 2 the numbers are skewed.
>
> The documentation clearly allows this (although there is not an example of 
> this type of annotation in the documentation, so I wonder if this is what we 
> meant?):
>
>> From the documentation:
>
>
> Annotating individual gene products according to attributes of a complex is 
> especially useful for molecular function annotations in cases where a complex 
> has an activity, but not all of the individual subunits do. (For example, 
> there may be a known catalytic subunit and one or more additional subunits, 
> or the activity may only be present when the complex is assembled.) Molecular 
> function annotations of complex subunits that are not known to possess the 
> activity of the complex must include the entry contributes_to in the 
> Qualifier column.
>
> Note that contributes_to is not needed to annotate a catalytic subunit. 
> Furthermore, contributes_to may be used for any non-catalytic subunit, 
> whether the subunit is essential for the activity of the complex or not.
>
>
>