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Here, we surveyed bioinformatics software tools for predicting cooperative transcription factor. Transcriptional regulation of gene expression is one of the major mechanisms for cells to respond to environmental and physiological changes. This kind of regulation is usually accomplished by cooperative transcription factors (TFs). The cooperativity among TFs enables cells to use a relatively small number of TFs in establishing the complex spatial and temporal patterns of gene expression. Therefore, identifying cooperative TFs is helpful for uncovering the mechanisms of transcriptional regulation.