Various signaling pathways are activated in molecular networks of diseases. To reveal the network pathways in epithelial-mesenchymal transition (EMT) and cancer stem cells (CSCs), the molecular networks and gene expression in diffuse- and intestinal-type gastric cancer (GC) have been analyzed. The network pathways of GC were analyzed by Ingenuity Pathway Analysis (IPA). The new causal network analysis of the probe sets of which gene expression have significant differences between diffuse- and intestinal-type GC in RefSeq data that are publicly available in cBioPortal Cancer Genomics identified 75 canonical pathways, 67 regulator effects and 866 causal networks in diffuse- and intestinal-type GC. Since these pathways are involved in several damage responses and RNA virus infection, focused analysis on oxidative stress response has been performed. NRF2-mediated oxidative stress response network included molecules related to Regulation of EMT by growth factors pathway and Production of nitric oxide and reactive oxygen species. Activation of Ras/ERK pathway was predicted in diffuse-type GC, whereas activation of NRF2 was predicted in intestinal-type GC. MicroRNAs which have direct relationships (RNA-RNA interactions: microRNA targeting) included mir-10, miR-1264 (and other miRNAs w/seed AAGUCUU), miR-142-5p (and other miRNAs w/seed AUAAAGU), mir-149, mir-155, mir-345, mir-497, miR-5087 (miRNAs w/seed GGUUUGU), mir-637, and mir-8. Adverse Outcome Pathway (AOP) related to chronic reactive oxygen species and human treatment-resistant gastric cancer has been developed.