Bisphenol A replacement chemicals can result in toxicity to neuronal cells, however, the underlying mechanisms are not well characterized. Transcriptome analysis was conducted in the neuronal SH-SY5Y human cell line following exposure of cells to either bisphenol F (BPF) or bisphenol S (BPS) at a concentration of 0.1 nM. Transcriptome data were used to predict which diseases were associated with bisphenol exposure using sub-network enrichment analysis. There were 305 subnetworks perturbed by BPF and 279 subnetworks perturbed by BPS. Top gene sets altered by BPF included urticaria, gastric lesion, attention deficit disorder, familial Mediterranean fever, malocclusion, and lupus erythematosus while for BPS, top gene sets included chronic urticaria, polymyositis, genital herpes, and hypergammaglobulinemia. There were 164 common diseases identified between BPF and BPS datasets. These included protein regulators of androgen deficiency, cerebral toxoplasmosis, metabolic alkalosis, panic attack, T-helper lymphocyte infiltration and vitiligo. Data can be re-used in regulatory toxicology to characterize biomarkers of exposure and elucidate common molecular responses to bisphenol replacements.