altrenative gene symbols
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burak kutlu ▴ 200
@burak-kutlu-1561
Last seen 6.4 years ago
Hi Is there a way to convert non-HUGO gene symbol identifiers to entrez gene or other ids? Example: ACSL1 aka ACS1; LACS; FACL1; FACL2; LACS1; LACS2; ACSL1 Thanks in advance -burak [[alternative HTML version deleted]]
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 7.7 years ago
United States
Hi Burak, You can always use the ALIAS2EG and the SYMBOL mappings in the organism annotation packages. So for example using the human package org.Hs.eg.db: library(org.Hs.eg.db) IDs = c("ACS1","LACS","FACL1","FACL2","LACS1","LACS2","ACSL1") #1st use ALIAS2EG to get entrez gene IDs for these EGs = mget(IDs, org.Hs.egALIAS2EG, ifnotfound=NA) #have a look at these: EGs #At this point you can already see that these all map to the same gene ID #BUT, you can get the most popular symbol by using the SYMBOL mapping: mget(as.character(EGs[1]),org.Hs.egSYMBOL, ifnotfound=NA) Hope this helps, Marc burak kutlu wrote: > Hi > Is there a way to convert non-HUGO gene symbol identifiers to entrez gene or other ids? > Example: > ACSL1 aka ACS1; LACS; FACL1; FACL2; LACS1; LACS2; ACSL1 > Thanks in advance > -burak > > > > [[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 > >
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