Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are rare diseases with a prevalence that has been increasing over the past three decades. The unsatisfactory outcome of these diseases has encouraged a great amount of research attention and discussion. Currently, to the best of our knowledge, studies on transcriptome screening and molecular mechanisms of the pathogenesis of GEP-NETs are limited. In this review, we have summarized the signaling network of GEP-NETs and the recent meta-analysis-related studies, and we have discussed the potential research direction for GEP-NETs, especially based on computational analysis.