[BioC] Fwd: Re: which package can do GSEA for no model organism

[Ana Conesa]

Hi

You can do GSEA with FatiScan (www.babelomics.org) with any
annotation file provided by the user. If you do not have the
annotation  for your non-model species you can generate it yourself
with Blast2GO (www.blast2go.org) provided you have sequence data, or
try to fetch them from the B2G-FAR (www.blast2go.org) site which
contains annotation data for over 2000 species, of course, most
non-model.

Hope this is of use to you

Ana


>
>
>---- Mensaje Original ----
>De: naomi at stat.psu.edu
>Para: bioconductor at stat.math.ethz.ch
>Asunto: RE: [BioC] Fwd: Re:  which package can do GSEA for no model
>organism
>Fecha: Mon, 29 Jun 2009 13:06:40 -0400
>
>>
>>>To: Pengcheng Yang <yangpc at ioz.ac.cn>
>>>From: Naomi Altman <naomi at stat.psu.edu>
>>>Subject: Re: [BioC] which package can do GSEA for no model organism
>>>Cc:
>>>Bcc:
>>>X-Eudora-Signature: <work>
>>>Date: Mon, 29 Jun 2009 13:06:22 -0400
>>>
>>>Dear Pengcheng,
>>>You cannot really talk about enrichment unless you have categories 
>>>for your genes.
>>>
>>>Usually, we use a program such as BLAST to align the unigenes to
>the 
>>>nearest model organism,
>>>and assign GO categories to the best hit.  But this may leave you 
>>>with 3 problems - 1) there will be lots of
>>>unigenes with no hit  2) there are usually several genes in the 
>>>model organism with multiple hits  3) until functional studies are 
>>>available for your organism, you can never know if the gene has the
>
>>>same function in your organism and the model organism.
>>>
>>>--Naomi
>>>
>>>At 07:20 AM 6/29/2009, you wrote:
>>>>Hi,
>>>>As far as I know, currently, GO analysis packages are based on
>>>>commercial platforms. How can I do GSEA analysis for the
>customized
>>>>array of no model organisms using existed packages? For example,
>an
>>>>array constructed based on unigenes, and the organism's genome has
>not
>>>>yet been sequenced.
>>>>
>>>>Regards
>>>>
>>>>--
>>>>Pengcheng Yang
>>>>
>>>>_______________________________________________
>>>>Bioconductor mailing list
>>>>Bioconductor at stat.math.ethz.ch
>>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>Search the archives: 
>>>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>Naomi S. Altman                                814-865-3791 (voice)
>>>Associate Professor
>>>Dept. of Statistics                              814-863-7114 (fax)
>>>Penn State University                         814-865-1348
>(Statistics)
>>>University Park, PA 16802-2111
>>
>>Naomi S. Altman                                814-865-3791 (voice)
>>Associate Professor
>>Dept. of Statistics                              814-863-7114 (fax)
>>Penn State University                         814-865-1348
>(Statistics)
>>University Park, PA 16802-2111
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>Search the archives: http://news.gmane.org/gmane.science.biology.inf
>ormatics.conductor
>>

-------------------------------------------
Ana Conesa, PhD
Bioinformatics Department
Centro de Investigación Príncipe Felipe
Avda. Autopista Saler 16
46013 Valencia Spain
http://bioinfo.cipf.es/aconesa
===========================================