Question: Microarray Gene Annotation
6
gravatar for Harsh
9.0 years ago by
Harsh70
Harsh70 wrote:

Hi everyone, I know the concept of multiple probe ids matching to single gene but, Is it possible that single affymetrix probe id matches to different genes in microarray?

ADD COMMENTlink modified 4.8 years ago by Biostar ♦♦ 20 • written 9.0 years ago by Harsh70
7
gravatar for Fred Fleche
9.0 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

[?]

For instance you have the probe 207739_s_at that match several genes (> 10) of the [GAGE][1] family. [?][?] You have also the probe 217365_at that match several member genes (> 5) of the [PRAME][2] family.

[?]

[?]

[?]

ADD COMMENTlink written 9.0 years ago by Fred Fleche4.3k
5
gravatar for Nathan Harmston
9.0 years ago by
Nathan Harmston1.1k
London
Nathan Harmston1.1k wrote:

This is definitely the case, a single probeset can contain a majority of probes which map to more than one location in the genome.

So I used SCAMPA, http://web.bioinformatics.ic.ac.uk/scampa/section.html?id=5

To do this, the tool has pre-defined thresholds for each of its levels, but you should be able to hack the source to define them yourself.

Of course, these corrections are sensitive to the genome-build you are using.

HTH

ADD COMMENTlink written 9.0 years ago by Nathan Harmston1.1k

expression array probe sets shouldn't really be mapped to the genome though - as those arrays detect RNA signal, right?

ADD REPLYlink written 8.6 years ago by Shigeta460

but those RNAs have to come from somewhere ... and if the probe hits exons from different genes then this definitely poses a problem due to reliable measurements

ADD REPLYlink written 8.6 years ago by Nathan Harmston1.1k
5
gravatar for Neilfws
9.0 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

It depends to some degree on the array platform but yes, to reiterate what has already been said, probes can match to more than one location. This can be due to duplication within the genome: for example, the 5'-end of the X chromosome is very similar to the Y chromosome, so probesets such as 218951_s_at (from the HG-U133A platform) match both.

There are tools to deal with this, but one approach is to download the relevant data from e.g. UCSC or Affymetrix and process it with a custom script to remove probesets with > 1 location.

ADD COMMENTlink written 9.0 years ago by Neilfws48k
4
gravatar for Khader Shameer
9.0 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Recently published tool GATExplorer was very useful for me to do probe to gene mapping. You can either use their server or download the files for microarray probe mapping.

ADD COMMENTlink modified 9.0 years ago • written 9.0 years ago by Khader Shameer18k
3
gravatar for Will
9.0 years ago by
Will4.5k
United States
Will4.5k wrote:

Yes, and this can be annoying when doing downstream annotation like KEGG pathways, etc. For example, if one probe says MapK is going Up and another says MapK is going down, how should I annotate this on a "gene-centered" graph like GO or KEGG.

My solution has been to use the "BrainArray" custom CDFs. These are created, and updated weekly, to reconstruct the affy-probesets so that each probeset matches a SINGLE ID. They have a build for UniGene (every probeset matches to a single UniGene ID), Entrez Gene, Entrez Protein, and dozens of others.

I've found that this make my downstream annotation much easier when I'm dealing with gene and protein level annotations. The only problem is that you need to have the RAW CEL data to use these CDFs.

Hope that helps, Will

ADD COMMENTlink written 9.0 years ago by Will4.5k
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