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. This evidence concerns the gene KAT2B and yang deficiency.