Workflow for functional analysis of differential gene core modules: KEGG, GSEA, and GO enrichment

Question

[mizzika]

Hello Biostars community,

I'm learning about enrichment analysis and would like to validate my approach for identifying the functions of differential gene core modules. Here's my proposed workflow:

1. Perform differential gene expression analysis
2. Conduct KEGG pathway enrichment on differentially expressed genes (DEGs)
3. Run GSEA KEGG analysis on all genes
4. Construct a Protein-Protein Interaction (PPI) network using DEGs
5. Extract core modules from the PPI network
6. Perform KEGG enrichment on genes in the core PPI modules
7. Identify intersection genes from the three enrichment results (steps 2, 3, and 6)
8. Conduct GO analysis on the intersection genes

Questions:

1. Is this a valid approach for identifying functions of differential gene core modules?
2. Are there any critical steps I'm missing or should consider adding?
3. What are the advantages and limitations of this method?
4. Can you recommend any specific tools or R packages for these analyses?
5. Are there any recent publications that have used a similar approach?

I appreciate any feedback, suggestions, or resources you can provide. Thank you!