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How to retrieve full gene names and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any other software or language)?

Is it possible vice versa: having full gene names or IDs get HUGO names or the other annotation data?

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  • $\begingroup$ Try DAVID. It has a gene ID converter option. There are many other Gene ID converters. $\endgroup$
    – WYSIWYG
    Feb 2, 2015 at 6:43
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    $\begingroup$ I'm voting to close this question as off-topic because it is not about biology. $\endgroup$ Feb 3, 2015 at 7:13

2 Answers 2

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I would recommend just downloading the database, which HUGO allows you to do free of charge.

The HUGO website has a "downloads" tab at the top that takes you to the following page

http://www.genenames.org/cgi-bin/statistics

You will see a table of statistics relating to how many protein- or non-protein-coding genes there are catalogued, etc.

Under the tables is a section called Complete dataset download links -- this is the section you want (unless you only want a subset of the data - but why not get it all!)

This plain text file (once uncompressed) can be loaded into R (or any other language) to be parsed and analysed as per your requirements.

It is worth updating the version you download quite regularly, as they update the HUGO database with new/updated info quite regularly.

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Install bioconductor and use this library: http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html

You can access BioMart which lets you translate between different ID types

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