I have a set of RNA data, 2 strains and three conditions. I did the mapping and Deseq analysis in geneious using our genome. But I ran into a problem that I'm struggling to resolve. I'm able to use KEGG with the FASTA Protein sequences to determine what types of processes are occurring in my different conditions. But I need to do gene enrichment on my differential data. But my locus tags, HF677_RS08395, are unique to my organism and are not recognized by most of the gene enrichment softwares out there. Ok, so I have my gene ID's and I can use enrichr, but some of my significantly differentially expressed genes have no gene symbol. I have little coding capabilities and not a lot of free time to learn how to use the coding software's out there. I'm wondering if anyone else has done gene enrichment on RNA data from unique environmental bacteria? How did you do it?
@all Performing gene ontology (GO) enrichment analysis for bacteria with unique locus tags and missing gene symbols can be challenging, but there are some tools and workarounds you can consider:
Remember that in the case of unique or less-studied organisms, functional annotation can be a labor-intensive process, and you may not always find exact matches for gene symbols. However, you can still gain valuable insights into the functions of your genes and perform enrichment analyses based on functional categories and GO terms. Additionally, collaborating with experts in the field or bioinformatics can greatly assist in this process.
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