Downstream analysis of DEG for non-model organisms.

Question

[georgii.vdovin]

Hello, has anyone here ever done downstream analysis on differentially expressed genes in non-model organisms? I'm working with the axolotl, and I am wondering what tools and with which identifiers people would typically work with.

[dthorbur]

Please provide more information in your questions. You have tagged GO and KEGG, but there is no mention of why these tags are here so I'm working on an assumption.

Assuming want to do GO and KEGG enrichment analyses, you could assign these annotations with to your transcriptome or proteome using tools like Blast2GO and here is a list of potential KEGG mapper tools. Then any of the numerous available enrichment tools will work. Personally, I like g:Profiler2.

In addition, there are many other useful tools at your disposal. BLAST is always a good starting point in comparative genomics and proteomics, InterProScan can add useful annotations, anchored and unanchored synteny tools, and OrthoFinder is useful to find orthologous sequences in other genomes that may be better annotated than your target species.

[georgii.vdovin]

Yes, I meant enrichment analyses; this helped, thank you!