Finding gene doubles in a list of genes

Question

[Jack]

Hello,

Suppose you are given a list of genes like this: MLL CYP2R1 MIR548AN TM9SF2 GALC DEXI CLEC16A RMI2 SHC1 etc...

and you have to check this list for those genes that have different names but actually are the same gene. What DB's would you use for that?

[cristina_sabiers]

good question....I have get many times same problem like in proteomic I get like 4 different names to the same gen and at end you don't know what to do with them because isn't like I want to split them manually.

[GenoMax]

Are these identifiers supposed to be from a single organism or multiple?

Answer 1

[Jean-Karim Heriche]

You can also get gene name synonyms with the EnsEMBL API e.g. to get gene names from UniProt for a given EnsEMBL gene:

 my $Ensgene = $gene_adaptor->fetch_by_stable_id($EnsemblID);
 my @uniprots = @{$Ensgene->get_all_DBLinks('Uniprot%')};

For human genes, the reference is HGNC from which you can download a table including synonyms.

Answer 2

[mastal511]

You need a table of gene synonyms for the organism you are working with.

Here is a link to a previous discussion on biostars: /https://www.biostars.org/p/1378/

[microfuge]

Just an addition that uniprot also provides synonyms in their flat file, can be easily parsed out.

Answer 3

[biofalconch]

You could use RefSeq, taking into account that

The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins

You can find the download links here

Have a good day :)

EDIT 1: Also, following Jean-Karim Heriche's suggestion, you can also make ID conversions depending on what type of IDs you have. You just need a way to compare tables, might be easily done in R or mySQL