Hi, I installed KEGG.db and org.Hs.eg.db packages. I could not find any function linking KEGG IDs / KEGG pathway Names to Refseq accession. I want to obtain a list like this: $notch_delta_signalling [1] "NM_002405" "AL133036" "NM_003260" "NM_004316" "NM_005077" "NM_005078" "NM_012486" "NM_004557" "NM_006161" "NM_005618" "NM_020999" "AF038196" "AA775404" "AK000144" "NM_007318" [16] "NM_007319" "NM_015383" "AW247193" "AA503101" "U94354" "H49418" "NM_000021" "AI961337" "AA583350" "NM_000214" "NM_019074" "NM_017617" "NM_016941" "NM_000435" "NM_000447" [31] "AL050141" "AI334327" "NM_002226" "NM_000890" $p53_signalling [1] "NM_002307" "NM_002392" "NM_003352" "NM_002745" "AI167145" "AI218142" "NM_004324" "NM_003633" "NM_013229" "AA845428" "AB036063" "NM_006024" "NM_005427" "NM_005446" "NM_005657" [16] "NM_007194" "U09579" "T79183" "NM_006878" "NM_006880" "NM_006881" "NM_006882" "AI796137" "NM_000051" "NM_000076" "NM_000077" "NM_000156" "AJ276888" "NM_001274" "NM_000546" [31] "NM_002066" "H93075" "AL157438" Any suggestions ? Thanks Viki S [[alternative HTML version deleted]]

here is a partly complete function that addresses this concern. you have two problems with your query. first the question is not organism-independent. second you need to know the specific tokenization of pathway names used in the KEGG.db package kpname2rs = function(pn="p53 signaling pathway", orgpref="hsa", genepack="org.Hs.eg.db") { pid = get(pn, revmap(KEGGPATHID2NAME)) nexts = get(paste(orgpref, pid, sep=""), KEGGPATHID2EXTID) unique(unlist(mget(nexts, org.Hs.egREFSEQ))) } the result of kpname2rs() with the sessionInfo given below has length 325 and includes a few of the results that you gave. the code has to be altered to deal appropriately with different organisms and to make fewer assumptions on the mapping packages used. R version 2.12.0 Patched (2010-10-15 r53331) Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] org.Hs.eg.db_2.4.6 KEGG.db_2.4.5 RSQLite_0.9-2 [4] DBI_0.2-5 AnnotationDbi_1.11.9 Biobase_2.10.0 [7] weaver_1.15.0 codetools_0.2-2 digest_0.4.2 On Fri, Oct 29, 2010 at 9:46 AM, Viki S <isvik at="" live.com=""> wrote: > > Hi, > I installed KEGG.db and org.Hs.eg.db packages. I could not find any function linking KEGG IDs / KEGG pathway Names to Refseq accession. I want to obtain a list like this: > > $notch_delta_signalling > ?[1] "NM_002405" "AL133036" ?"NM_003260" "NM_004316" "NM_005077" "NM_005078" "NM_012486" "NM_004557" "NM_006161" "NM_005618" "NM_020999" "AF038196" ?"AA775404" ?"AK000144" ?"NM_007318" > [16] "NM_007319" "NM_015383" "AW247193" ?"AA503101" ?"U94354" ? ?"H49418" ? ?"NM_000021" "AI961337" ?"AA583350" ?"NM_000214" "NM_019074" "NM_017617" "NM_016941" "NM_000435" "NM_000447" > [31] "AL050141" ?"AI334327" ?"NM_002226" "NM_000890" > > $p53_signalling > ?[1] "NM_002307" "NM_002392" "NM_003352" "NM_002745" "AI167145" ?"AI218142" ?"NM_004324" "NM_003633" "NM_013229" "AA845428" ?"AB036063" ?"NM_006024" "NM_005427" "NM_005446" "NM_005657" > [16] "NM_007194" "U09579" ? ?"T79183" ? ?"NM_006878" "NM_006880" "NM_006881" "NM_006882" "AI796137" ?"NM_000051" "NM_000076" "NM_000077" "NM_000156" "AJ276888" ?"NM_001274" "NM_000546" > [31] "NM_002066" "H93075" ? ?"AL157438" > > Any suggestions ? > > Thanks > Viki S > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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 >