[BioC] Fwd: Re: which package can do GSEA for no model organism
Pengcheng Yang
yangpc at ioz.ac.cn
Wed Jul 1 05:42:23 CEST 2009
Hi Marc,
We are working on Locust (Locusta Migratoria).
Marc Carlson 写道:
> Hi Pengcheng,
>
> What organism are you working on?
>
>
> Marc
>
>
>
> Pengcheng Yang wrote:
>
>> Hi,
>> Thanks for your zealous reply.
>> Sorry for my inadequate question description.
>> We have done the GO annotation for the Unigenes using interproscan. I
>> have written several R functions to do GO/KEGG enrichment analysis for
>> our customized array based on the fisher-exact test and chi-square test.
>> But the analysis is limited to the third level of GO hierarchy. More R
>> functions are needed if I do GSEA at deeper level. So I wonder that why
>> "AnnotationDbi" package or "Category" do not develop a function to
>> create customized annotation packages or objects. The packages/objects
>> contain the annotations of the specific species' Unigenes or other
>> sequences from unsequenced organisms. The annotation contain user
>> defined classes, such as GO, KEGG, IPR, etc. Once the packages/objects
>> is created the GSEA can be done through existed packages, such as
>> GOstats, topGO, etc.
>>
>> Thanks, Ana. FatiGO++ really can do the work, but we need run in batch.
>> So program is need.
>>
>>
>>
>>
>> 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
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>>>>> 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
>>> ===========================================
>>>
>>> _______________________________________________
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>>>
>>>
>>>
>>
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>>
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>
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--
Pengcheng Yang
PhD Candidate
IOZ,CAS
email: <yangpc at ioz.ac.cn>
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