Geneset enrichment in non-model organism with DAVID

Question

[pbigbig]

Hi everyone,

I have an assembled whole transcriptome and several transcriptomes from different development stage of a non-model fish. Basically, I would like to see which gene, gene groups and/or pathways is specifically expressed in which development stage, so there are differential expression analysis and gene enrichment analysis need to be performed.

I wonder if this is a correct way that I use only orthologs of my fish vs zebrafish (given that they are closely related in taxonomical term) and then use genelist based on zebrafish hits for geneset enrichment analysis on DAVID? Is there another feasible approach for this kind of analysis on non-model organism? Any advice and suggestion are greatly welcomed

Thank you very much!

Phuong

[Guangchuang Yu]

maybe you can use clusterProfiler.

[pbigbig]

Thanks for your suggestion!

Answer 1

[Pappu]

You can try GSEA of Broad.

[pbigbig]

Thanks for your suggestion!