We discovered that: (1) thymic carcinomas overexpressed HDAC9 and NFATC1, which could be potential therapeutic targets and associated with the neuroendocrine phenotype in the thymus; (2) genes involved in thymic development, including PAX9 and SIX1, were markedly downregulated in thymic carcinomas; and (3) thymic carcinoma had distinct gene expression patterns that might be related to the global methylation changes. The gene discussed is NFATC1; the disease is thymic carcinoma.