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DNA methylation is identified as an elaborate epigenetic element to regulate binding of transcription factor to gene promoter region. With latest highthroughput technology, it is convenient to accurately test methylation level in experiment, which opens a door to investigate how methylation affects transcription factor. In this study, a general model is presented to depict methylation function, where parameters of model are fixed by analysis of relativity between transcription factor binding scores in promoter regions and gene expression levels. In neuroblastoma cell, with the deduced model, 10 transcriptional factors were found to be apparently affected by methylation of promoter regions.