This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Looking for clean list of gene names for UCSC's HG19

I'm trying to make sense of some data and analysis I've inherited. It's a big mess. The results include some gene names that are clearly corrupted ("Excel genes", etc.).

Therefore, for starters, I want to determine a "clean" list of the "gene universe" that was used for the analysis. All I have been able to ascertain is that the reference gene data used came from UCSC's HG19 build.

By "clean" I mean that the list I'm looking for should

  • be complete
  • contain no synonyms
  • consist of identifiers belonging to one and only one system of nomenclature

Of course, the ideal would be a simple file, published by UCSC, consisting of one gene name per line, no duplicates, but after much searching I have not been able to find such a file.

Does such a file exist? If not what would be the closest I could find?

Thanks in advance!

gene genome
• 4,224 views • link
updated by Ram Ram • written by kynnjo • kynnjo

3 answers

You can use the method suggested by Gian, or use UCSC's mysql access.

The query:

SELECT DISTINCT geneSymbol from kgXref kx;

or, directly from the command line:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e 'SELECT DISTINCT geneSymbol from kgXref'
• 0 views • link
written by Ram Ram

This

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz

then

zcat refFlat.txt.gz | cut -f 1 | sort -u
• 0 views • link
updated by Ram Ram • written by Lemire Lemire

Log in to answer this question.

More posts like this