An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization

MOTIVATION To understand transcription regulatory mechanisms, it is indispensable to investigate transcription factor (TF) DNA binding preferences. We noted that the generally acknowledged information of functional annotations of TFs as well as that of their target genes should provide useful hints in determining TF DNA binding preferences. RESULTS In this contribution, we developed an integrative method based on the Nearest Neighbor Algorithm, to predict DNA binding preferences through integrating both the functional/structural information of TFs and the interaction between TFs and their targets. The accuracy of cross-validation tests on the dataset consisting of 3430 positive samples and 7000 negative samples reaches 87.0% for 10-fold cross-validation and 87.9% for jackknife cross-validation test, which is a much better result than that in our previous work. The prediction result indicates that the improved method we developed could be a powerful approach to infer the TF DNA preference in silico. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.