Question

Standardizing gene symbols

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Nithisha ▴ 10

@nithisha-14272

Last seen 6.8 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!

R • 2.3k views

ADD COMMENT • link updated 7.1 years ago by Gordon Smyth 52k • written 7.1 years ago by Nithisha ▴ 10

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

ADD REPLY • link 7.1 years ago Simon Anders ★ 3.8k

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Hi Simon,

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

ADD REPLY • link 7.1 years ago Nithisha ▴ 10

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markus.riester ▴ 130

@markusriester-9875

Last seen 2.5 years 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

ADD COMMENT • link updated 7.1 years ago by Gordon Smyth 52k • written 7.1 years ago by markus.riester ▴ 130

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Thank you! I shall try this out as well.

ADD REPLY • link 7.1 years ago Nithisha ▴ 10

score 2 · Accepted Answer · 2017-11-23

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Gordon Smyth 52k

@gordon-smyth

Last seen 11 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".

ADD COMMENT • link 7.1 years ago Gordon Smyth 52k

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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!

ADD REPLY • link 7.1 years ago Nithisha ▴ 10