I have an assembled transcriptome. I performed analyses on this transcriptome to extract candidate sequences involved in the production of a substance. Then, I annotated both sets of data using the Eggnog Mapper tool. This is an example of my result table enter image description here Being new to bioinformatic, I am currently stuck on which statistical analysis to perform to determine the functions most involved in the production of the substance, and what other analyses can I perform with these two sets of data? The eggnog annotation results didn't give the gene ID.
I have tried the overrepresentation test a functional enrichment analysis for COGs (Clusters of Orthologous Groups); COGs annotation and redundancy in a table and to compare between the two set of data; using the R code https://yulab-smu.top/biomedical-knowledge-mining-book/enrichment-overview.html#gsea-algorithm , with clusterProfiler but it seems that it may not work because I don't have gene IDs in my annotation results eggnog doesn't give it. With which tools or code can I perform this test, please?
