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Background: By studying the correlation of histone modifications and the process of transcription, it has been showed that there is very universal correlation between histone modification and gene expression.Besides, different combination of histone modifications has the special function in the process of transcription initiation and repression.So, we analyzed the correlation and predicted the level of gene expression using the increment of diversity combined with the discriminant.Methods: According to the CpG content of the promoter and various modification sets of different combination of modifications around the TSS(transcription start site), we extracted characteristic parameters to build the source of diversity for each promoter type.For a given gene, we calculated the increment ofdiversity(ID) with the source, and combined IDs with quadratic discriminant analysis to predict its expression level.This method is based on a comprehensive consideration ofhistone modifications.Results: As a result, our results indicated that different combination of histone modifications contributes to specific promoter to facilitate gene expression process.Meanwhile, the results also showed that the correlation between histone modifications and gene expression is effectively described with a considerable prediction accuracy of the gene expression.Conclusions: All in all, using various histone marks, we analyze the effect of histone modifications in the transcription process.The features to which we apply the IQDQ method (increment of diversity combined with quadratic discriminant analysis) are remarkable characters showing the correlation between histone modifications and gene expression, providing an available clue to the full research about the histone modification .