[BioC] gene function assessment

[Sean Davis]

On Fri, Feb 10, 2012 at 7:48 PM, Abhishek Pratap <apratap at lbl.gov> wrote:
> Unfortunately the gene id's are local to us.  So there will be no
> mapping between them to RefSeq, Entrez etc.

Assuming that you mean that you do not have GenBank or any other
public ID, I see no option for you except to start BLASTing to get
some useful ID.

Sean


> 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
>>>> >
>>>> >        [[alternative HTML version deleted]]
>>>> >
>>>> > _______________________________________________
>>>> > Bioconductor mailing list
>>>> > Bioconductor at r-project.org
>>>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> > Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor