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Microarray Probe id Annotation

During annotation of microarray data if same probe id represents multiple genes which one should be considered or as more significant?

e.g

Agilent probe id: A_32_P101313

Bioconductor package used : hgug4111a.db

Using Bioconductor I have got the following genenames for the same probe ID

  1. PTPLAD2 : protein tyrosine phosphatase-like A domain containing 2
  2. focadhesin FOCAD
microarray
• 5,154 views • link
updated by Ram Ram • written by anur89 • anur89

You need to show the code which led to this result. According to the GEO entries for this platform (GPL886 and GPL7263), that probe ID maps only to PTPLAD2.

• 1 views • link
updated by Ram Ram • written by Neilfws Neilfws

In R using the the library hgug4111a.db

> library(hgug4111a.db)

> probeset<-c("A_32_P101313")
> probes.anno <- select(hgug4111a.db, keys=probeset, columns=c("GENENAME", "SYMBOL"), keytype="PROBEID")

> print(probes.anno)
       PROBEID                                                GENENAME  SYMBOL
1 A_32_P101313 protein tyrosine phosphatase-like A domain containing 2 PTPLAD2
2 A_32_P101313                                              focadhesin   FOCAD
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updated by Ram Ram • written by anur89 • anur89

1 answer

The FOCAD and PTPLAD2 genes are next to each other (but on opposite strands). Your best bet is to take the probe sequence and BLAT it to the genome (very easily done with the UCSC genome browser). Then you can inspect and investigate why or if it really is complementary to two specific genes. If it matches both genes identically, then the answer to your question: "if same probe id represents multiple genes which one should be considered or as more significant?" is that the genes are indistinguishable, and you'll have to do a different/better experiment to tell them apart.

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written by seidel seidel

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