[BioC] GO enrichment for genome-wide analysis

[Sean Davis]

On 1/10/06 8:42 AM, "James W. MacDonald" <jmacdon at med.umich.edu> wrote:

> burak kutlu wrote:
>> Hi, My understanding is that GOstats implements the GO term
>> enrichment analysis for studies using microarrays (where the lib
>> argument is passed to "GOHyperG" to define the microarray-specific
>> environment, therefore the gene universe). I was wondering if there
>> is a readilly-available function for determining GO term significance
>> that uses the GO terms from the whole genome rather than the GO terms
>> from the genes represented on an array.
> 
> I don't think you will find this anywhere, because it doesn't make
> sense. The idea behind GOHyperG is similar to the canonical 'ball and
> urn' scenario used in basic stats to explain the Hypergeometric
> distribution.
> 
> The goal is to determine the probability of reaching into an urn
> containing a certain number of black and white balls, removing x balls
> and having n of those balls be white.
> 
> Your question is akin to asking the probability of reaching into an urn
> containing black and white balls, removing x balls and having n of those
> balls be white, but based on the relative proportion of black and white
> balls in the world, instead of the proportion of black and white balls
> in the urn. Since the proportion of black and white balls may be quite
> different in the urn as compared to the world, you cannot generalize
> like that.

As Jim points out, it's a bad idea to do what you propose, but if you really
want to, there ARE online and standalone applications that will allow you to
do this.  One example is at:

http://david.niaid.nih.gov/david/ease.htm

But there are several others.

Sean