Probe Set Annotation for Illumina HumanMethylation450 Beadchip

For probe set annotation in the Illumina Infinium HumanMethylation450 Beadchip array, we used the expanded annotation table provided by Price et al. [28 (link)]. This file was used for associating gene and transcript with respective CpG site, the distance to the closest transcription start site and the occurrence of any single nucleotide polymorphism (SNP) loci in the CpG site. CpG sites were excluded from the analysis if carrying a known SNP locus or if located outside the area 1500 bp upstream or downstream from the transcriptional start site (TSS1500 interval). The probe set annotation file provided by Affymetrix (Affymetrix Inc., Santa Clara, CA) was used to associate a gene transcript with probes on the Affymetrix chip. On this array, probes may be annotated to more than one individual transcript.