Question: How To Associate Cpg Coordinate With The Gene Names Or Entrez Id
2
gravatar for hdy
4.8 years ago by
hdy90
United States
hdy90 wrote:

I am dealing with methylation data and see those entries are describe as CpG/CpH coordinate (UCSC hg19, Feb 2009), like: cg00013618 and cg00027083. How can I retrieve the gene names or ids from these coordinate information?

methylation • 7.2k views
ADD COMMENTlink modified 8 weeks ago by RamRS19k • written 4.8 years ago by hdy90
3
gravatar for GANI
4.8 years ago by
GANI220
United States
GANI220 wrote:

I see that based on the probe Identifiers, you were using Illumina Methylation data. What specific platform are you using (27k or 450k)? Also, what tools/language are you using to perform the analysis?

If you are working in R, you can use the following package to retrieve the corresponding gene information for 27k platform.

http://www.bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation27k.db.html

or the following package for 450k platform

http://www.bioconductor.org/packages/2.13/data/annotation/html/IlluminaHumanMethylation450k.db.html

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by GANI220

I am using 27K now but probably will also head into 450K as well, thank you for your advice and I do use R. Do you know, if I am dealing with 450k, what tools may help and give me results?

ADD REPLYlink written 4.8 years ago by hdy90
1

I just updated my post with the 450k annotation as well.

ADD REPLYlink written 4.8 years ago by GANI220

Here's the R-code.

source("https://bioconductor.org/biocLite.R")
biocLite("IlluminaHumanMethylation450k.db")

library(IlluminaHumanMethylation450k.db)
CpG_annotation <- as.list(IlluminaHumanMethylation450kSYMBOL[mappedkeys(IlluminaHumanMethylation450kSYMBOL)])
ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by sjorsvanheuveln50
1
gravatar for Isaac Joseph
2.1 years ago by
Isaac Joseph80
Berkeley, CA USA
Isaac Joseph80 wrote:

So, for posterity, to save time and do something roughly equivalent, just do biocLite('FDb.InfiniumMethylation.hg19')instead of the above.

Details: the above appears to be deprecated; I received the following error:

    >biocLite("IlluminaHumanMethylation450k.db")

...

    Error : .onLoad failed in loadNamespace() for 'IlluminaHumanMethylation450k.db', details:
      call: NULL
      error: 'fun' is defunct.
    Use 'FDb.InfiniumMethylation.hg19' instead.
    Use 'FDb.InfiniumMethylation.hg18' instead.
    Use 'mapToGenome() function in minfi or methylumi' instead.

, suggesting that I use one of these other databases.

ADD COMMENTlink written 2.1 years ago by Isaac Joseph80
1

Plot twist: said posterity now includes me, as I forgot how to do this, and moreover, forgot that I knew how to do this, so Google®ed it and came upon this question again.

ADD REPLYlink written 23 months ago by Isaac Joseph80
0
gravatar for Kevin Blighe
8 weeks ago by
Kevin Blighe31k
Republic of Ireland
Kevin Blighe31k wrote:

Same issue here and just became really [really] tired of these annotation packages becoming outdated.

You can easily obtain the 450k methylation annotation data from Illumina's website, where it should always remain and not vanish into thin air:

Kevin

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by Kevin Blighe31k
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