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?
3 answers
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.
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
Log in to answer this question.
-
Python methylation position visualisation
written by gmodlovver •
-
How to get all microRNA target genes?
written by Katarina •
-
snp list from Affymetirx microarray files
written by avichaireich •
-
How to retrieve sequences of genes list at a time from a fasta file
written by evafinegan •
-
Using GOplot with data from Gene Ontology Resource
written by basch •
-
From consensus sequence with variants to protein
written by Maxime •
-
Nucleotide to amino acid conversion of multiple sequences
written by lokraj2003
-
differential expression from multiple sequencing panels
written by glocke01
-
Extract genes from gene list
written by Bioblazer
-
Comparing genome assemblies
written by xandinho2468 •
