[Genome] gene walking & Unigene cluster mapping

[Guoliang Xing]

Dear Genome help team,

    I want to code some Perl programs to compare different microarray
signals on the same genes using UCSC genome browser annotation data. I'd
like to download relevant gene track info in MySQL dataabse and run in
local machine mode.

    Let's say Affy Expression array U133 plus2 vs. Affy U95, they have
different probe coverages, but some of the probes mapped to the same gene.
My intuition is to map different probes on the two different arrays to a
common Unigene cluster id, and then run my statistical comparison based on
common cluster ID, gene by gene.

    I know UCSC browser has the Affy array mapping info.

    But I don't know which track or mySQL UCSC table is the current gold
starndard for gene annotation.

    Please advise.

    Thanks

    Guoliang