Let's say you have an RNA-seq counts matrix for two experimental groups, and you have already generated your table of differentially expressed genes. Generally speaking, what are the best ways to interrogate this dataset?
The ones I can think of:
- Gene ontology enrichment
- WGCNA and/or MEGENA for co-expression networks: modules; eigengenes, eigengene networks
- ARACNE for transcription factor-target networks
- Key driver analysis (i.e., which hub gene in WGCNA/MEGENA/ARACNE has the highest connectivity; what other ways are there to define key drivers?)
- HOMER for regulatory binding sites
Any other methods, reviews, papers are highly appreciated!