[BioC] gene function assessment

[Sean Davis]

On Fri, Feb 10, 2012 at 3:50 PM, Abhishek Pratap <apratap at lbl.gov> wrote:
> Chlamydomonas.  I was reading a bit more about this ..so I guess what I
> might need to do is associate GO ID for each gene in my set and the may be
> use GOSeq like packages but I am not sure how should I go about associating
> GO ID's to genes.

And what, exactly, are your gene ids?  Are they Entrez Gene IDs,
RefSeq, Genbank, or something else?

> On Fri, Feb 10, 2012 at 12:46 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> What organism?
>>
>> On Fri, Feb 10, 2012 at 2:48 PM, Abhishek Pratap <apratap at lbl.gov> wrote:
>> > We have identified a set of genes to be differentially expressed between
>> > treatment and control.  The current gene annotation doesnt have
>> functional
>> > information about the gene.
>> >
>> > What we would like to do is asses the biological functions of these
>> genes(
>> > may be based on GO and then cluster them). I was wondering if there is
>> > something already out there to do so in semi automated way.
>> >
>> > I am thinking of blasting them against pfam  or be myhits dbase but
>> wanted
>> > to take your opinion.
>> >
>> > PS  : cross posted on biostar mailing list :
>> >
>> http://biostar.stackexchange.com/questions/17332/functional-assessment-of-genes
>> >
>> > Thanks!
>> > -Abhi
>> >
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>> >
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