[BioC] Gene Lists and Genomes

[Steve Lianoglou]

On Thu, May 5, 2011 at 1:06 PM, Radhouane Aniba <aradwen at gmail.com> wrote:
>
>
> 2011/5/5 Steve Lianoglou <mailinglist.honeypot at gmail.com>
>>
>> Hi,
>>
>> On Thu, May 5, 2011 at 12:25 PM, Radhouane Aniba <aradwen at gmail.com>
>> wrote:
>> > Thanks Tim,
>> >
>> > Actually I have a predicted list of miRNA binding sites targetting
>> > specific
>> > genes in 4 genomes.
>> >
>> > What I am trying to find is the characteristics of these Genes {g} for a
>> > specific genome {G} in term of GO enrichement and KEGG enrichment.
>> >
>> > My starting point is a file with a list of ENSEMBL IDs, just that, no
>> > annotation and no scores, just the gene names.
>> >
>> > I am looking for the right package to do that, topGO for example seems
>> > to
>> > not accept only gene names, annotation is needed as well as other
>> > details, I
>> > am acually reading about all these packages that make gene enrichment
>> > analyses.
>>
>> It seems as if you can use GOstats for this purpose, but you'd first
>> need to convert these IDs to entrez id (which you can do using the
>> appropriate org.*.eg.db pacakge (org.Hs.eg.db if we're talking about
>> human, for example).
>>
>> In addition to this 'target list' you have, you'll need a appropriate
>> way to define "the universe" of gene id's to use for testing.
>
>
> What is the universe of gene ids ? what does is it means ?

You are supplying some set of genes that have been "picked" (you hope)
non randomly. From what set of genes did you use to pick these from?

That set of all possible genes you could have "picked" from is the
universe -- the (size and makeup of the) universe you pick will affect
your results.

For instance ... were you looking at miRNA's that were expressed only
in a particular cell type? If so, did you look for targets that were
only expressed in that cell type, or did you look for targets from the
set of all "known" genes? Why did you pick your universe in the way
you did?

You get the idea ...

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact