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The N-terminal tails of the core histones are subject to mutiple covalent modifications. The histone code hypothesis suggests that multiple histone modifications act in a combinatorial fashion to affect gene transcription. To investigate the combinatorial patterns of histone modifications at the promoter region of gene, Bayesian network method was used to analyze the causal relationships among 12 histone modifications in Saccharomyces. cerevisiae. The results show that there are 13 combinatorial patterns. In general, there are the causal relationships among some modifications which are strongly correlated. The modifications of H3K4Meland H3K18Ac are directly related to gene transcription. Other modifications affect indirectly gene transcription by H3K4Mel and H3K18Ac. Some causal relationships attribute to the modifying enzymes.