KEGG and GO analysis with Daphnia magna Uniprot IDs

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4.3 years ago

Hannes ▴ 60

Hi Community,

does anyone know how I can run a ORA (over representation analysis) or GSEA (gene set enrichment analysis) for Daphnia magna Uniprot IDs?

In the past I have worked with Zebrafish and ENSEMBL Gene IDs using R packages biomaRt and clusterProfiler to get the job done. However, as far as I know clusterProfiler is not able to run its default analysis with Daphnia magna.

I found this publication which claims to have done that via the KEGG and GO websites. However when I check them, neither http://geneontology.org nor https://www.genome.jp/kegg/catalog/org_list.html do support/contain Daphnia magna. Both sites only have entries for Daphnia pulex (which of course was not mentioned in the EST publication, nor the reference genome they used for mapping but that's a different story ...)

Basically I would like to run my analysis in R to be able to automate the process but I have no idea which tools I can use right now as I am not working with a standard model organism. Can someone help me out here?

For the beginning I think it would help already if I could map orthologues genes from D. magna to D. pulex. Thx a lot in advance already! :)

RNA-Seq R • 1.0k views

ADD COMMENT • link updated 10 months ago by Penbiotox • 0 • written 4.3 years ago by Hannes ▴ 60

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Hi, did you ever find a solution for this? I’m struggling with this myself!

ADD REPLY • link 10 months ago by Penbiotox • 0

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You can look into GeneSCF: https://github.com/genescf/GeneSCF

ADD REPLY • link 10 months ago by GenoMax 148k

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Thank you!

ADD REPLY • link 10 months ago by Penbiotox • 0

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