Gene ID conversion for pathway enrichment analysis of differentially expressed genes

Question

[abhilashtripathi10]

Hello Community Members

I am facing problems in setting up pathway enrichment analysis for the differentially expressed genes because of problems with Gene Ids. I tried using DAVID but the species that I am using is not listed there.

In brief, I used the annotation file (ggf3) from https://bacteria.ensembl.org/Desulfovibrio_alaskensis_g20_gca_000012665/Info/Index/ for RNA seq data analysis. I have the list of up and down-regulated genes. I am trying to do gene enrichment pathway analysis for the up and down-regulated genes using various online platforms such as DAVID, CPDB, and Shinygo. The problem that I am facing is that none of these online platforms are accepting the gene ids from the gene annotation file I obtained from ebi. All online platforms require Ensembl gene ids and I am unable to convert.

Species: Desulfovibrio alaskensis G20

Genome Annotation file link: https://bacteria.ensembl.org/Desulfovibrio_alaskensis_g20_gca_000012665/Info/Index/

Any help will be greatly appreciated and very helpful in my research.

[Kevin Blighe]

Now posted on Bioconductor: https://support.bioconductor.org/p/9135952/

Answer 1

[Ridha]

You can use gprofiler. It accepts gene symbols and I think bacteria is included. Also, there is a tool to convert gene ids.

[abhilashtripathi10]

Thank you for the reply. But my organism of interest (Desulfovibrio alaskensis G20) is not listed there. Do you know any other platforms?

[LauferVA]

are there any species in the options you listed that have a homolog for every gene in your species? see where i am going with that?

ultimately you just need the software to perform numerical computations, the labels are irrelevant ... if you are defining the pathways themselves, and you have the total number of transcripts, etc. etc. you should be able to trick one of the softwares into doing its job ... you could also look at the implementation of fgsea etc. (https://github.com/ctlab/fgsea) and implement a version flexible enough yourself