Multiple USCS_gene_name for one CpG

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6.6 years ago

janhuang.cn ▴ 210

I am using the IlluminaHumanMethylation450kanno.ilmn12.hg19 Bioconductor package to get the annotation for some CpG sites. But I found that UCSC_RefGene_Name for some CpGs has more than one gene.

There are two scenarios.

1) The same gene is listed multiple times. For example,

UCSC_RefGene_Name of cg09315878 is "SDF4;SDF4". This is splice variants. I wonder if I could interpret this as cg09315878 is on SDF4 gene?

2) Different genes are listed for one CpG. For example,

UCSC_RefGene_Name of cg02716826 is "SUGT1P1;AQP3". I am not sure why and how to interpret this.

cpg methylation annotation • 1.8k views

ADD COMMENT • link updated 3.0 years ago by wuhan9281 • 0 • written 6.6 years ago by janhuang.cn ▴ 210

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Tagging: genecats.ucsc

ADD REPLY • link 6.6 years ago by GenoMax 141k

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Hi! I am also puzzled with this. Have you got it?

ADD REPLY • link 3.0 years ago by wuhan9281 • 0

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