derivation of Ref Gene Group

[Susan Huse]

Hi,

I am working with the Infinium 450K DNA Methylation arrays. These include information about the various methylation sites.
Three of the fields included are UCSC_REFGENE_NAME, UCSC_REFGENE_ACCESSION, and UCSC_REFGENE_GROUP.
The possible values for the RefGene Group are TSS1500, TSS200, 5'UTR, Body, 1stExon, and 3'UTR.

The annotation also includes another field: REGULATORY_FEATURE_GROUP, which is not from UCSC, possibly it is from EMBL, but I am not yet certain.
The group values for this field are gene associated, gene associated cell-type specific, promoter associated, promoter associated cell-type specific, non-gene associated, non-gene associated cell type specific, and unclassified, unclassified cell-type specific.

When ran the comparison across the methylation sites of the UCSC TSS1500, TSS200 and the gene bodies, I did not get meaningful correlations with the promoters and genes from the other source. In other words, they gene definitions don't overlap well and the UCSC TSS locations don't correspond with their promoter regions.

The genes from the UCSC Genome Browser are documented as from RefSeq with cross-referencing. How were the TSS1500 and TSS200 derived -- what was the definition of the beginning of the gene? Was that at the 5' or 3' end of the 5' UTR? How was the gene body defined - the coding of the protein? how was the 1st exon defined, etc. I have searched the web and read many publications but have so far been unable to track this down. Any information you can provide on the full derivation of these annotations would be very helpful.

Sue Huse
Alpert Medical School
Brown University

[Pauline Fujita]

Hello Sue,

Thank you for your interest in the Genome Browser. Unfortunately these
are not distinctions made by us so you will have to contact your array
vendor directly regarding the answers to these questions.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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