How can multiarray results have more than 1 gene name for each row?
3
0
Entering edit mode
5.4 years ago
basch • 0

I am currently looking at a paper that are using a panel of 357 genes to test some illness. I want to retrieve the list of these 357 genes to make some own analyses in my own data-set (RNA-seq experiment)

However, when I look at the list of genes that they provided, the list has 357 rows, which seems correct, but some of the rows have more than one gene name, example below:

  • GBP2
  • CTSS
  • PVRIG /// STAG3

What does this third item mean? I will have to translate the genes into orthologues in another species, and inputing two genes like this, separated with "///" won't work. Which one of them should I choose, or maybe both?

microarray RNA-Seq • 1.1k views
ADD COMMENT
2
Entering edit mode
5.4 years ago
Ahill ★ 2.0k

The triple slash notation is used by Affymetrix annotation files for probesets that map to multiple gene identifiers. The paper likely used those annotation files as a source of gene mappings. See here:

Each row after the first row contains annotations for a single probe set. All annotations for that probe set are contained in that single row. In some fields, such as the protein domain annotations, there can be more than one annotation for a single probe set. In this case, the multiple values are separated by the string " /// ".

This means the corresponding probeset probably can't distinguish between PVRIG and STAG3 expression due to cross hybridization. If mapping to orthologues the cautious approach would be to include both.

ADD COMMENT
1
Entering edit mode
5.4 years ago

Looking at the human genome, you can see that those two genes are very closed , maybe they are regulated by the same elements (always co-expressed ?) that could explain why they put them together ? https://www.ncbi.nlm.nih.gov/gene/10734

ADD COMMENT
0
Entering edit mode

But how should I input this list into Ensembl Biomart? The rows with more than one gene will be invalid. Also, the number of genes is then more than what they state in the paper.

Is this a microarray thing that I don't understand?

ADD REPLY
0
Entering edit mode

Was this a custom array or a commercial one? If it is commercial can you say what array?

ADD REPLY

Login before adding your answer.

Traffic: 1883 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6