The main merits of this study are as follows: (1) by reanalyzing RNA-Seq data, we identified the responsible targets for Yang deficiency (KAT2B, NFKB2, CREBBP, GTF2H3) and Yin deficiency (JUNB, JUND, NGLY1, TNF, RAF1, PPP1R15A) in Chinese medicine theory; (2) functional annotations for the representative targets in both body constitution (Yang or Yin deficiency) were provided; and (3) R-based machine learning approaches used in this investigation might be further adopted for unveiling the potential genetic polymorphisms related to the Chinese medicine theory. The gene discussed is RAF1; the disease is yang deficiency.