Question: Retrieving all entrez identifiers that are annotated in KEGG pathways
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6.6 years ago by
Guest User12k
Guest User12k wrote:
Dear all, Is there any way to get all entrez identifiers that are annotated with KEGG pathways? Actually I am using GOStats package in R to perform KEGG pathway enrichment analysis.. In general, for each KEGG pathway term there is a list of annotated hgnc symbols or entrez identifiers.. For all KEGG pathway terms we must have one list of entrez identifiers. I want to have that list... What I am doing write now is as follows: library(biomaRt) library("GO.db") library("KEGG.db") library("GOstats") library("hgu133plus2.db") library("EMA") library("fdrtool") library("org.Hs.eg.db") ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") x <- hgu133plus2PATH mapped_probes <- mappedkeys(x) b<-getBM(attributes=c("hgnc_symbol"),filters="affy_hg_u133_plus_2",val ues=mapped_probes,mart=ensembl) Is it the correct way to do that? Thanks in advance.. :) -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 6.6 years ago by ANIRBAN BHAR60 • written 6.6 years ago by Guest User12k
Answer: Retrieving all entrez identifiers that are annotated in KEGG pathways
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gravatar for ANIRBAN BHAR
6.6 years ago by
ANIRBAN BHAR60
ANIRBAN BHAR60 wrote:
*right now On Sat, Mar 2, 2013 at 2:20 PM, Anirban [guest] <guest@bioconductor.org>wrote: > > Dear all, > > Is there any way to get all entrez identifiers that are annotated with > KEGG pathways? Actually I am using GOStats package in R to perform KEGG > pathway enrichment analysis.. In general, for each KEGG pathway term there > is a list of annotated hgnc symbols or entrez identifiers.. For all KEGG > pathway terms we must have one list of entrez identifiers. I want to have > that list... > > What I am doing write now is as follows: > library(biomaRt) > library("GO.db") > library("KEGG.db") > library("GOstats") > library("hgu133plus2.db") > library("EMA") > library("fdrtool") > library("org.Hs.eg.db") > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > x <- hgu133plus2PATH > mapped_probes <- mappedkeys(x) > > > b<-getBM(attributes=c("hgnc_symbol"),filters="affy_hg_u133_plus_2",v alues=mapped_probes,mart=ensembl) > > Is it the correct way to do that? > > Thanks in advance.. :) > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org. > -- ______________________________________ Anirban Bhar Department of Bioinformatics University of Goettingen Goettingen, Germany [[alternative HTML version deleted]]
ADD COMMENTlink written 6.6 years ago by ANIRBAN BHAR60
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