Extracting Ucsc Canonical Gene Information

Question

[Ian]

As a simple method of associating genes to ChIP-seq binding regions I want to employ the UCSC canonical gene set, in order to avoid the inclusion of multiple transcripts per gene.

Using the UCSC table browser I am looking to extract the following information:

chr [ chrom from hg18.knownCanonical]

start [ chromStart from hg18.knownCanonical]

end [ chromEnd from hg18.knownCanonical]

strand [ strand from hg18.knownGene]

ucsc_id [ name from hg18.knownGene]

gene symbol [ best place? at present geneName from hg18.refFlat]

I can get these items by selecting the items from the tables (shown between [ and ]).

I can get gene symbol from the Refseq related tables, but this restricts symbols to the refseq set of genes (possibly not a bad thing...).

How does the UCSC browser link a gene symbol (e.g. SYN3) to the knownGene track, instead of displaying uc003amx.1?

This is currently a human question.

Thanks!

Answer 1

[Ian]

Silly me! I found the answer here on biostars:

Ucsc Gene Name Question

I needed geneSymbol from hg18.kgXref.

Thanks Mary for her answer!

If there is an alternative please post it here!

[Mary]

You are welcome :)