Nice work, but as you say, the following: It is common to see these gene sets being referred as pathways and it is for this reason that GSEA is also known as pathway analysis. Will really lead to communication problems with biologist, but you already admit that in the sentence following this one :)

For a very long long time, Pathways are the word used by biologists for defined signalling cascades inside cells, to used the same word for a clustered gene set is quite confusing.

Your approach is very data driven and as it is you are ignoring a vast sea of literature out there that investigates the relation between signalling pathways and target mRNAs by doing research into (among others) transcription complexes directly (i.e. using CHIP [0]) (like they do i.e. here: [1]). I get that for computer scientists this is perhaps the fastest way to results but I feel such research can be done in a smarter way, by teaming up with biologists. Don't you agree?

[0] https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation

[1] http://www.ncbi.nlm.nih.gov/pubmed/24695361