Best way to define the Background Genes to compare overlapping DE genes from microarray and RNAseq

Question

[Valeria Mafra]

I have several lists of DE genes, some of them from microarray and others from RNAseq.

I have tried to use the GeneOverlap library in R to perform and test the overlapping between two or more gene lists, but I do not know how to define a full list of genes to use as my gene background.

Could I use all genes in the genome or get a common list from all datasets, by filtering the same gene features and selecting features that only exist in both RNA-seq and microarray?

[Thomas]

Hello there. Sorry, I am a little confused, what exactly are you trying to determine by using GeneOverlap in this way?

[Valeria Mafra]

Hi Thomas, I am looking for common DE genes that are shared between two experiments, so the GeneOverlap compare two gene lists and then uses Fisher's exact test to find the statistical significance. Considering the contigency table 2x2, I have the number of differentially expressed genes to each list but I need to chose the gene universe (DE + Not DE). Since I wish to compare microarray x RNAseq studies, I have two options in this case: 1- Universe is all genes in the genome 2- Universe is only the expressed genes What is the best option in this case?

Answer 1

[Benn]

Usually, for microarrays, you take all genes that are present on the microarray as a background.

For RNAseq I usually use all genes in the genome. So if you use something like featureCounts, all genes that are used for this tool.

[Manuel Landesfeind]

... and to do comparison between RNA-Seq and micro-array one would use the intersection of both background lists.

[Valeria Mafra]

Thank you for your answer guys!