Hello Biostars, I am analyzing the RNA-seq data of a non-model plant (de novo) but after assembly, differential gene expression, and GO mapping I need a reliable pipeline for GO enrichment and network analysis. I have seen some papers using Cytoscape (BINGO, Enrichment Map, ...) but I do not know how to prepare my data for these tools. Most of the software for these reasons just do these kind of analysis for model organisms. Please give me your experiences about de nove transciptome analysis? Many thanks,
There's nothing fundamentally different between doing GO enrichment and network analysis in model organisms compared to others. The main difference is data availability, genes in model organisms are usually well annotated with respect to function and other information and can easily be linked to each other by e.g. protein or genetic interactions. For a new organism, you can make use of this information by transferring it via orthology. For example, for GO, you can annotate your genes with GO terms from orthologs in well-annotated closely-related species.