Question: Microarray Probe id Annotation
0
gravatar for anur89
4.4 years ago by
anur890
anur890 wrote:

 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 • 2.8k views
ADD COMMENTlink modified 4.4 years ago by seidel6.8k • written 4.4 years ago by anur890

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.

ADD REPLYlink written 4.4 years ago by Neilfws48k

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

 

 

ADD REPLYlink written 4.4 years ago by anur890
0
gravatar for seidel
4.4 years ago by
seidel6.8k
United States
seidel6.8k wrote:

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.

ADD COMMENTlink written 4.4 years ago by seidel6.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 996 users visited in the last hour