[BioC] gene function assessment

[Abhishek Pratap]

Unfortunately the gene id's are local to us.  So there will be no
mapping between them to RefSeq, Entrez etc.

-Abhi

On Fri, Feb 10, 2012 at 4:45 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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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