I work in a clinical research studying global methylation in normal and cancer tissue using the Illumina 450k array.
My question is pretty straightforward: I am looking for resources (ie. documentation, articles, etc.) that detail how the probe annotations have been derived for the manifests/anotation files available. I am interested in specific experiments and procedures used to come up with these annotations.
Specifically, I would like to know how Enhancer status was defined (what assay(s) were used? How was it determined these regions were associated with the listed gene?).
In case it is helpful, I have been using the manifest implemented in the Bioconductor package minfi.
Clinical Research Division
UPDATE 7/7/15: An Illumina rep pointed me to a handy bulletin on the Illumina website with details on the annotation. It says Enhancer status is determined informatically by Encode, however it is still not clear which track(s) correspond to what was used. Also it would be great to find a reference to the specific algorithm(s) in question. S