I appreciate your motivation

So, now , what should I be looking for ? should I now focus on the found pathways ? or the genes of the 8 modules ? and now

Look at both the pathways and the genes in the modules.

Bioinformatics analyses can only take us so far. At a certain point, one must stop the analysis and simply take a look over the results and start to make conclusions. Try to see the pathway and gene enrichment analyses as merely guides to help you form your conclusions.

If in a paper it is implied that gene x is affecting the process, so then just mentioning it in my report , would be enough ?

This would be just an in silico analysis; so, not proof. If you want to say something like 'gene X is affecting pathway Y', then you will likely require in vitro validation (depending on the journal to which you are aiming to submit the work).

And How to know if the my results worth to claim it is an acceptable work ?

This will be the job of the reviewers performing the peer review. We cannot really comment here because we cannot see your results and code. Some general pointers:

• use adjusted p-value thresholds when choosing your final list of enriched pathways
• implement a minimum number of genes for enrichment (i.e., if a pathway is enriched from just 2 genes, is that meaningful?)
• be aware of the reputation of the databases against which you are enriching your data. KEGG and GO are reputable and are constantly curated; others, less so. If using GO, be aware of evidence codes: A: Go annotation reliability ?

Kevin