How To Annotate Methylation 450K?

Question

[liu4gre]

I have the file from encode, with the calculated beta values and probe id. I am wondering how to map these probes to genes symbol? And how to determine their locations, such as promoter, 3'UTR or gene body?

Thanks

[Tanvir Ahamed]

I am wonder do you have any success over your question!! I am at same situation.

Answer 1

[Devon Ryan]

You could start with the IlluminaHumanMethylation450k Bioconductor package, which contains mappings for at least part of what you're looking for (maybe all of it, I haven't checked).

[Charles Warden]

I think this is probably sufficient. I know IMA provides region-level calculations for the categories that you listed, but that isn't a Bioconductor package and might be using something else.

If not, I know for certain they are included in the .bpm file that you can download here:

https://support.illumina.com/array/array_kits/infinium_humanmethylation450_beadchip_kit/downloads.ilmn

The website was being slow for me, but it should work. If not, you can just use the copy of the .bpm file included with the COHCAP demo dataset (the standalone version of COHCAP also adds these labels at the CpG site level, but this is probably not the most efficient way to accomplish this single task):

http://sourceforge.net/projects/cohcap/

Once you delete some of early and final lines (or write code to ignore those lines), this is just a tab-delimited text file that you can parse.

[Shicheng Guo]

Hi Charles, Can you give me some introduce to .bmp files (methylation 450K, such as GPL13534_HumanMethylation450_15017482_v.1.2.bpm.gz)? It is binary files, I didn't find too much introduction on the interenet.

[Charles Warden]

If you don't want to parse the Illumina annotation files, you can use these commands for the Bioconductor code:

library("IlluminaHumanMethylation450kanno.ilmn12.hg19")
data("IlluminaHumanMethylation450kanno.ilmn12.hg19")
annotation.table = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)

Answer 2

[Researcher]

Were anyone able to get this 450K annotation file? Please do share with me too.

Answer 3

[Vassilis]

Here is the updated link to download the csv. The columns specification can be found here.