Question: Fwd: Re: which package can do GSEA for no model organism
0
gravatar for Ana Conesa
10.3 years ago by
Ana Conesa340
Ana Conesa340 wrote:
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 Investigaci?n Pr?ncipe Felipe Avda. Autopista Saler 16 46013 Valencia Spain http://bioinfo.cipf.es/aconesa ===========================================
annotation go organism assign • 678 views
ADD COMMENTlink modified 10.3 years ago by Pengcheng Yang40 • written 10.3 years ago by Ana Conesa340
Answer: Fwd: Re: which package can do GSEA for no model organism
0
gravatar for Pengcheng Yang
10.3 years ago by
Pengcheng Yang40 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@stat.psu.edu >> Para: bioconductor@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@ioz.ac.cn> >>>> From: Naomi Altman <naomi@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@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@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 > =========================================== > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Pengcheng Yang PhD Candidate IOZ,CAS email: <yangpc@ioz.ac.cn> [[alternative HTML version deleted]]
ADD COMMENTlink written 10.3 years ago by Pengcheng Yang40
Have you tried R-GSEA at http://www.broad.mit.edu/gsea/ which allows the use of standard or custom arrays and gene sets. Ian --- 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 >>>> 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 Investigaci?n Pr?ncipe Felipe >> Avda. Autopista Saler 16 >> 46013 Valencia Spain >> http://bioinfo.cipf.es/aconesa >> =========================================== >> >> _______________________________________________ >> 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 >> >> >> > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
ADD REPLYlink written 10.3 years ago by Ian Sudbery50
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 >>>> 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 Investigaci?n Pr?ncipe Felipe >> Avda. Autopista Saler 16 >> 46013 Valencia Spain >> http://bioinfo.cipf.es/aconesa >> =========================================== >> >> _______________________________________________ >> 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 >> >> >> > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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
ADD REPLYlink written 10.3 years ago by Marc Carlson7.2k
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