Pseudogene Identification in HGU133PLUS2 using BioConductor

Question

[emiliomastriani]

Dear guys, I just finished to conduct the differential expression analysis of a public dataset from GEO, where researchers used the HGU-133 PLUS 2.0 to retrieve the samples. So, I opted for the hgu133plus2.db to make the annotation. Now, I got a set of differential expressed genes (I am on bioconductor, limma, etc). Now, I want to know which of them are pseudogenes. Of course, I don't want check one-by-one querying some db... it's boring and long procedure. Please, any smart approach? Thanks

Answer 1

[Kevin Blighe]

You can do this via biomaRt, as I show here: A: Affymetrix Human Genome U133 Plus 2.0 Array

Your value of filter may differ, depending on whether your lookup is affy_hg_u133_plus_2 (the probe IDs) or external_gene_name (gene symbols).

There are upward of 40,000 pseudogenes in total in GENCODE, I believe; so, more pseudogenes than protein coding genes are known.

Kevin