[BioC] gene function assessment

[Sean Davis]

On Fri, Feb 10, 2012 at 9:14 PM, Abhishek Pratap <apratap at lbl.gov> wrote:
> Hi Sean
>
> I see. I was wondering if I can scan my sequences against InterPro
> (EBI) and get the GO information from there. Any package in
> bioconductor or may be I need to use their API.

I don't think Bioc has that, but I'd love to hear otherwise.  You can
certainly try Interpro, but in your situation, I'd be working toward
mapping your sequences to a rich data source like Entrez Gene or
Ensembl.  There are a number of routes to that goal, but all of them
start with some sequence similarity searching.

Sean


> On Fri, Feb 10, 2012 at 6:10 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>> 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]]
>>>>>> >
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>>>>>
>>>>>        [[alternative HTML version deleted]]
>>>>>
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