Statistically overrepresented gene types from Differentially expressed genes.

Question

[EVR]

Hi,

I have DESeq2 results from RNA-seq after comparing Control and Treated samples and obtained a list of differential expressed genes(DEG). My DEG includes genes of a different type. i.e. protein-coding, lincRNA, snoRNA, tRNAs etc.,

I want to identify statistically overrepresented gene types from this result table. Is there any package available to do identify the statistically overrepresented gene category. please guide me

Thanks in advance

Answer 1

[i.sudbery]

Almost any package that can do GO enrichment can take user defined categories of gene, rather than categories defined by the GO consortium.

For RNA-seq I recommend correcting for sequencing bias' particularly if you have gene types of different lengths (e.g. snoRNAs). Thus, I'd recommend the goseq package. Their manual has a section on defining your own gene categories.