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Background: It is well known that histone modifications can control gene expression, and the data of histone modifications have grown exponentially by the next-generation sequencing techniques.Based on these data, many theoretical works for epigenetics researches could be proceed.But dealing with such big data is quite difficult and time-consuming, which really is a challenge for computational biology.The epigenetic modification is cell-type specific, so we chose one important cell type, the human embryonic stem (ES) cell, to study the relationship between histone modifications and gene expression levels.