Gene ID conversion for pathway enrichment analysis of differentially expressed genes

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 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: bacteria.ensembl.org/Desulfovibrio_alaskensis_g20_gca_000012665/Info/Index/

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


Pathwayenrichment


GeneIdconversion

• 121 views

link

updated 6 hours ago by

Ridha

▴

20

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


Login
before adding your answer.

Traffic: 1211 users visited in the last hour



Source link