Dear all: As you have known, "AnnBuilder" provide the well-annotation of GO and KEGG. I would like to know the index between genes and pathways in Yeast. Namely, I want to know whether the gene is belong to which pathway or not? However, I cannot find the functions in "AnnBuilder" package might link the genes to pathways. Can any body give me some suggestions? Thank you for the help. Shih-Te ------------------------------------------------ Shih-Te Yang, Ph.D. student Bioinformatics Research Center Institute of Biochemistry School of Life Science National Yang-Ming University Tel:+886-2-28267000*5666 Fax:+886-2-81461062 E-mail:g38903040@ym.edu.tw MyWeb: http://binfo.ym.edu.tw/styang/

>As you have known, "AnnBuilder" provide the well-annotation of GO and KEGG. >I would like to know the index between genes and pathways in Yeast. Namely, >I want to know whether the gene is belong to which pathway or not? However, >I cannot find the functions in "AnnBuilder" package might link the genes to >pathways. Can any body give me some suggestions? Have a look at the YEAST annotation package, where you will find links between ORF ids and GO and KEGG ids. > >Thank you for the help. > >Shih-Te >------------------------------------------------ >Shih-Te Yang, Ph.D. student >Bioinformatics Research Center >Institute of Biochemistry >School of Life Science >National Yang-Ming University >Tel:+886-2-28267000*5666 >Fax:+886-2-81461062 >E-mail:g38903040@ym.edu.tw >MyWeb: http://binfo.ym.edu.tw/styang/ > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

The functions are not in AnnBuilder, AnnBuilder's role in life is to construct annotation, not to use it. Most of the functions that use annotation (meta-data) packages are in the annotate package. So with BioC installed, something like library(reposTools) install.packages2("YEAST") library(YEAST) ?YEASTPATH2PROBE should get you most of the way there. There is no reason to use AnnBuilder unless you want to build your own, custom annotation data sets and if you do, then use AnnBuilder to construct them and proceed as above. Robert On Wed, Nov 19, 2003 at 09:30:21PM +0800, Shih-Te Yang wrote: > Dear all: > > As you have known, "AnnBuilder" provide the well-annotation of GO and KEGG. > I would like to know the index between genes and pathways in Yeast. Namely, > I want to know whether the gene is belong to which pathway or not? However, > I cannot find the functions in "AnnBuilder" package might link the genes to > pathways. Can any body give me some suggestions? > > Thank you for the help. > > Shih-Te > ------------------------------------------------ > Shih-Te Yang, Ph.D. student > Bioinformatics Research Center > Institute of Biochemistry > School of Life Science > National Yang-Ming University > Tel:+886-2-28267000*5666 > Fax:+886-2-81461062 > E-mail:g38903040@ym.edu.tw > MyWeb: http://binfo.ym.edu.tw/styang/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+