How to see if DEGs are grouped in genome?

Question

[Parham]

Hi,

In my experiment I compromise replication and transcription, then look into transcriptome for changes.

One thing that I would like to investigate is if the DEGs are significantly grouped in close-by loci through out genome or they are just scattered out in a random manner?

I would like to have your feedback on how to approach this question and which packages do you recommend?

I prefer to work under R environment if that's possible. The organism that I work on is S. pombe. Let me know if you need more information.

Thanks in advance,
Parham

[apelin20]

Well, depends on how many genes you got. If you are using cufflinks, it tells you the genomic chromosome/scaffold as well as nucleotide range the DEG is located on, so if you look at the DEGs you may visually be able to tell how close they are.

[Parham]

I was previously using cufflinks but then I switched to STAR and DESeq2 for the purpose. I will look into that. Thanks!

[apelin20]

Another idea is to export your annotation in BED, and then just write a quick grep script that will pull out the positions of the DEGs.

Answer 1

[Christian]

I ended up using the Perl script from de Preter et al. (2008), which worked quite nicely: Recommended tools for positional gene enrichment (PGE) analysis?

[Parham]

Yeah that looks convenient. However they don't have fission yeast genome in their data base unfortunately. Thanks for recommending though!