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Background  Various chromatin modifications, identified in large-scale epigenomic analyses, are associated with distinct phenotypes of different cells and disease phases. To improve our understanding of these variations, many computational methods have been developed to discover novel sites and cell-specific chromatin modifications. Despite the availability of existing methods, there is still room for further improvement when they are applied to resolve the histone code hypothesis. Hence, we aim to investigate the development of a computational method to provide new insights into  de novo  combinatorial pattern discovery of chromatin modifications to characterize epigenetic variations in distinct phenotypes of different cells.    Results  We report a new computational approach,  ChARM  ( C ombinatorial C h romatin Modification Patterns using  A ssociation  R ule  M ining), that can be employed for the discovery of  de novo  combinatorial patterns of differential chromatin modifications. We used  ChARM  to analyse chromatin modification data from the livers of normal (non-cancerous) mice and hepatitis B virus X (HBx)-transgenic mice with hepatocellular carcinoma, and discovered 2,409 association rules representing combinatorial chromatin modification patterns. Among these, the combination of three histone modifications, a loss of H3K4Me3 and gains of H3K27Me3 and H3K36Me3, was the most striking pattern associated with the cancer. This pattern was enriched in functional elements of the mouse genome such as promoters, coding exons and 5′UTR with high CpG content, and CpG islands. It also showed strong correlations with polymerase activity at promoters and DNA methylation levels at gene bodies. We found that 30 % of the genes associated with the pattern were differentially expressed in the HBx compared to the normal, and 78.9 % of these genes were down-regulated. The significant canonical pathways (Wnt/ß-catenin, cAMP, Ras, and Notch signalling) that were enriched in the pattern could account for the pathogenesis of HBx.    Conclusions    ChARM , an unsupervised method for discovering combinatorial chromatin modification patterns, can identify histone modifications that occur globally.  ChARM  provides a scalable framework that can easily be applied to find various levels of combination patterns, which should reflect a range of globally common to locally rare chromatin modifications.    Electronic supplementary material  The online version of this article (doi:10.1186/s12859-016-1307-z) contains supplementary material, which is available to authorized users.

ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining