Hi Chen Yue, To link genes to KEGG pathways try out this package: http://www.bioconductor.org/packages/2.5/data/annotation/html/KEGG.db. html KEGG.db is a AnnotationDbi package. Many kind of Metadata information is stored in such AnnotationDbi packages. So, if you understand to come along whit one AnnotationDbi you will be able to handle all the other AnnotationDbi. AnnotationDbi packages always end by ".db" in their name. To get you started: # install the package source("http://bioconductor.org/biocLite.R") biocLite("KEGG.db") # attach the package library(KEGG.db) # some man pages ?KEGG.db # basic man page ? ls("package:KEGG.db") # list all the object that exist in KEGG.db ?"KEGGEXTID2PATHID" # maybe the object you where looking for # some example ids <- c("7150","1281542","1274031") pathway = mget(ids, KEGGEXTID2PATHID, ifnotfound = NA) pathway Ps: This is what is written on the bioconductor homepages about AnnotationDbis ( http://www.bioconductor.org/overview ) : The Bioconductor project provides software for associating microarray and other g0enomic data in real time to biological metadata from web databases such as GenBank, LocusLink and PubMed (annotate package). Functions are also provided for incorporating the results of statistical analysis in HTML reports with links to annotation WWW resources. Software tools are available for assembling and processing genomic annotation data, from databases such as GenBank, the Gene Ontology Consortium, LocusLink, UniGene, the UCSC Human Genome Project (AnnotationDbi package). Data packages are distributed to provide mappings between different probe identifiers (e.g. Affy IDs, LocusLink, PubMed). Customized annotation libraries can also be assembled. Merry Christmas, Elmar -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of bioconductor- request@stat.math.ethz.ch Sent: 20 December 2009 13:00 To: bioconductor at stat.math.ethz.ch Subject: Bioconductor Digest, Vol 82, Issue 19 Send Bioconductor mailing list submissions to bioconductor at stat.math.ethz.ch To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/bioconductor or, via email, send a message with subject or body 'help' to bioconductor-request at stat.math.ethz.ch You can reach the person managing the list at bioconductor-owner at stat.math.ethz.ch When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioconductor digest..." Today's Topics: 1. how to get gene list after hyperGTest (Yue, Chen - BMD) ---------------------------------------------------------------------- Message: 1 Date: Sat, 19 Dec 2009 12:36:26 -0600 From: "Yue, Chen - BMD" <yuechen@bsd.uchicago.edu> Subject: [BioC] how to get gene list after hyperGTest To: <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <ad1fa15416eebc49a0fe4f8b0c8ad7c5158f35 at="" adm-="" exchvs04.bsdad.uchicago.edu=""> Content-Type: text/plain Hi, I'm wondering if someone can help me with the result extraction after hyperGTest in GOstats package. After I obtained the hyperGTest result, I also want to know what category each input gene associates with, for example a KEGG pathway. What function should I use? Or should I use another package? Thanks! Chen, Yue This email is intended only for the use of the individua...{{dropped:15}}