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Question:the CpG site corresponding to the gene name in IlluminaHumanMethylation450k

hello all, in lluminaHumanMethylation27k the CpG site cg00011459 corresponding gene name is PMM2 but in lluminaHumanMethylation450k the CpG site in lluminaHumanMethylation27k corresponding gene name is TMEM186;PMM2. it mean cg00011459 is in PMM2, or the cg00011459 is near the TMEM186 and PMM2.

450k methylation illumina array gene symbol
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updated by Kevin Blighe Kevin Blighe • written by jiang.hk.xm • jiang.hk.xm

1 answer

I am confident that the probe is targeting the same base on each chip, however, to understand why the annotation is different, you have to understand the region in question: TMEM186 and PMM2 share a bi-directional promoter due to their very close proximity. Thus, methylation in the region may affect both genes. This knowledge may only have come out post the release of the 27k and pre the release of the 450k.

I would encourage you to look at the supplier's information on both chips, too. For example, take a look here for the 450k where you cn download numerous types of information: https://support.illumina.com/array/array_kits/infinium_humanmethylation450_beadchip_kit/downloads.html

They should provide probe sequences and exact target regions.

Kevin

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written by Kevin Blighe Kevin Blighe

It been confirmed that a single CpG site that can affect both genes?

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written by jiang.hk.xm • jiang.hk.xm

If it's confirmed that it's a bi-directional promoter, then one can infer with confidence that methylation at the region is going to affect both genes. I agree with your sentiment that it's not concrete proof without doing wet-lab validation.

You may want to look deeper into the literature to find the study that initially highlighted evidence of this, but it may have been a whole genome screen and therefore buried in the supplementary. Here is the study that I found, which mentions the bi-directional promoter activity at this locus: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3082894/

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written by Kevin Blighe Kevin Blighe

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