Gene ID conversion for pathway enrichment analysis of differentially expressed genes
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19 days ago

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.

Pathwayenrichment GeneIdconversion • 569 views
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Now posted on Bioconductor: https://support.bioconductor.org/p/9135952/

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19 days ago
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.

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

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