Transcriptional alterations of the hub genes were confirmed except for Atg9a. Additionally, through modeling miRNA–mRNA-transcription factor interactions for the hub genes, we confirmed a transcription factor, Cebpa, is essential to regulate the expression of Rhobtb2. We did not find singificent singals in the prefrontal cortex responding to maternal prenatal nutritional deficiency. Here, RHOBTB2 is linked to nutritional deficiency disease.