Mapping gene symbols to gene names (org.Hs.eg.db?)

1

Entering edit mode

Tim Smith ★ 1.1k

@tim-smith-1532

Last seen 10.3 years ago

Hi, I was trying to map gene symbols to gene names using the org.Hs.eg.db package. I first convert the gene symbol to an entrez id, and then convert that to a gene name (example code below). However, during this process I can't get the gene names for some of the genes: -------------------------- library(org.Hs.eg.db) ### First two genes are ok... symbols <- c('JAK1','AATK','A2BP1','A2LD1') for(sym in symbols){ print('***') entrezid <- as.character(mget(sym,org.Hs.egSYMBOL2EG,ifnotfound=NA)) print(sym) print(entrezid) genename <- as.character(mget(entrezid,org.Hs.egGENENAME,ifnotfound=NA)) print(genename) } ------------------------- I don't get any gene names for the last two genes in this example. Is there a better way of doing this? Perhaps with some other function/package? thanks. [[alternative HTML version deleted]]

convert convert • 13k views

ADD COMMENT • link updated 10.6 years ago by James W. MacDonald 67k • written 10.6 years ago by Tim Smith ★ 1.1k

0

Entering edit mode

James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 37 minutes ago

United States

Hi Tim, >symbols <- c('JAK1','AATK','A2BP1','A2LD1') >select(org.Hs.eg.db, symbols, c("ENTREZID","GENENAME"), "ALIAS") ALIAS ENTREZID GENENAME 1 JAK1 3716 Janus kinase 1 2 AATK 9625 apoptosis-associated tyrosine kinase 3 A2BP1 54715 RNA binding protein, fox-1 homolog (C. elegans) 1 4 A2LD1 87769 gamma-glutamylamine cyclotransferase Best, Jim On 5/13/2014 6:38 AM, Tim Smith wrote: > Hi, > > I was trying to map gene symbols to gene names using the org.Hs.eg.db package. I first convert the gene symbol to an entrez id, and then convert that to a gene name (example code below). However, during this process I can't get the gene names for some of the genes: > > -------------------------- > > library(org.Hs.eg.db) > > ### First two genes are ok... > symbols <- c('JAK1','AATK','A2BP1','A2LD1') > > for(sym in symbols){ > print('***') > entrezid <- as.character(mget(sym,org.Hs.egSYMBOL2EG,ifnotfound=NA)) > print(sym) > print(entrezid) > > genename <- as.character(mget(entrezid,org.Hs.egGENENAME,ifnotfound=NA)) > print(genename) > > } > > > ------------------------- > > I don't get any gene names for the last two genes in this example. Is there a better way of doing this? Perhaps with some other function/package? > > > thanks. > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

ADD COMMENT • link 10.6 years ago James W. MacDonald 67k

0

Entering edit mode

Thanks Jim! On Tuesday, May 13, 2014 10:18 AM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Tim, >symbols <- c('JAK1','AATK','A2BP1','A2LD1') >select(org.Hs.eg.db, symbols, c("ENTREZID","GENENAME"), "ALIAS") ALIAS ENTREZID GENENAME 1 JAK1 3716 Janus kinase 1 2 AATK 9625 apoptosis-associated tyrosine kinase 3 A2BP1 54715 RNA binding protein, fox-1 homolog (C. elegans) 1 4 A2LD1 87769 gamma-glutamylamine cyclotransferase Best, Jim On 5/13/2014 6:38 AM, Tim Smith wrote: > Hi, > > I was trying to map gene symbols to gene names using the org.Hs.eg.db package. I first convert the gene symbol to an entrez id, and then convert that to a gene name (example code below). However, during this process I can't get the gene names for some of the genes: > > -------------------------- > > library(org.Hs.eg.db) > > ### First two genes are ok... > symbols <- c('JAK1','AATK','A2BP1','A2LD1') > > for(sym in symbols){ > print('***') > entrezid <- as.character(mget(sym,org.Hs.egSYMBOL2EG,ifnotfound=NA)) > print(sym) > print(entrezid) > > genename <- as.character(mget(entrezid,org.Hs.egGENENAME,ifnotfound=NA)) > print(genename) > > } > > > ------------------------- > > I don't get any gene names for the last two genes in this example. Is there a better way of doing this? Perhaps with some other function/package? > > > thanks. > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]

ADD REPLY • link 10.6 years ago Tim Smith ★ 1.1k

Login before adding your answer.