I'm just a freshman in the field of epigenetics. I have questions about methylation data analysis:
The data from Infinium HumanMethylation450 BeadChip will tell us which CpG sites are methylated or not, but I do not know the corresponding genes. so how do we tell which genes are methylated or not? which tools are appropriate to interpret this data? is QDMR useful for this purpose?
Thank you very much
Dear Ho Nguyen Tuong,
you can download the manifest of the HumanMethylation450 BeadChip directly from the Illumina Homepage (https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html). This manifest includes all information about the CpG sites, like the corresponding gene, and the chromosomal position.
As I have never worked with QDMR I cannot tell you if this tool is useful for this purpose. Usually, I use the ChAMP pipeline in R to analyse Illumina BeadChip data (https://www.bioconductor.org/packages/release/bioc/vignettes/ChAMP/inst/doc/ChAMP.html).
Greetings,
Julie Krainer
To determine the methylation level of the surrounding CpG sites near a particular 450K array locus, we usually recommend to perform targeted bisulfite sequencing. I attached slides here for your information.
you were basically asking how to map CpG site to its potentially regulated gene. The majority of HumanMethylation450 probes are located in promoters, so you just need to select the gene whose TSS (transcription start site) is closest to the CpG. However, if the CpG is located in the distal regulatory regions (such as enhancer), map CpG to gene is tricky, you could try GREAT (http://great.stanford.edu/public/html/)