Standardizing gene symbols
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Nithisha ▴ 10
@nithisha-14272
Last seen 6.1 years ago

Hello all,

I have a list of gene symbols that I obtained after querying CHEMBL and a separate list of gene symbols from querying datasets from GEO and using Limma on them.

When I try to compare both lists, I find that I cannot look for similar gene symbols as gene synonyms exist. An example would be for microtubule associated protein tau, I have the gene symbols "TAU", "MTBT1" and "MAPTL". Is there anyway I can standardize gene symbols so that I can see how frequently a gene symbol occurs?

Any advice would be appreciated!

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This depends on the organism (species). What is it?

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Hi Simon,

Some lists are from mice and some are from humans. Would this cause problems?

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@gordon-smyth
Last seen 4 hours ago
WEHI, Melbourne, Australia

The limma functions alias2Symbol() or alias2SymbolTable() do this conversion for you. For example, if you have a column called "Symbol" in your limma results, and you want to convert all the symbols to current official symbols, just use:

fit$genes$Official.Symbol <- alias2SymbolTable(fit$genes$Symbol, species="Hs")

For mouse symbols, use species="Mm".

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Thanks a lot Gordon. 

I do have a few questions though. For your code, I did not completely understand what 

fit$genes$Official.Symbol refers to. Is that pointing to a dataframe within another dataframe?

I used this:

dfl$Official_Symbol <- alias2SymbolTable(df$gene, species="Mm")

where df is a dataframe containing my Limma results and the column "gene" contains my gene symbols.

And I get this following error:

Warning message:
In alias2SymbolTable(df$gene, species = "Mm") :
  Multiple symbols ignored for one or more aliases

I wanted to know if I could do something about the warning?

Thank you!

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@markusriester-9875
Last seen 21 months ago
United States

For human symbols, HGNChelper might work for you:  
 

checkGeneSymbols(c("TAU", "MTBT1","MAPTL"))

      x Approved Suggested.Symbol

1   TAU    FALSE             MAPT

2 MTBT1    FALSE             MAPT

3 MAPTL    FALSE             MAPT

Warning message:

In checkGeneSymbols(c("TAU", "MTBT1", "MAPTL")) :

  x contains non-approved gene symbols

 

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Thank you! I shall try this out as well.

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