QBiC-Pred: Quantitative Predictions of Transcription Factor Binding Changes Due to Sequence Variants II

Non-coding genetic variants/mutations can play functional roles in the cell by disrupting regulatory interactions between transcription factors (TFs) and their genomic target sites. For most human TFs, a myriad of DNA-binding models are available and could be used to predict the effects of DNA mutations on TF binding. However, information on the quality of these models is scarce, making it hard to evaluate the statistical significance of predicted binding changes. Here, we present QBiC-Pred, a web server for predicting quantitative TF binding changes due to nucleotide variants. QBiC-Pred uses regression models of TF binding specificity trained on high-throughput in vitro data. The training is done using ordinary least squares (OLS), and we leverage distributional results associated with OLS estimation to compute, for each predicted change in TF binding, a p-value reflecting our confidence in the predicted effect. We show that OLS models are accurate in predicting the effects of mutations on TF binding in vitro and in vivo, outperforming widely-used PWM models as well as recently developed deep learning models of specificity. QBiC-Pred takes as input mutation data sets in several formats, and it allows post-processing of the results through a user- friendly web interface. QBiC-Pred is freely available at http://qbic.genome.duke.edu. Universal protein-binding microarray (PBM) experiments were performed for recombinant, epitope-tagged transcription factors from human, mouse, and A. thaliana. Briefly, universal PBMs involved binding of GST-tagged, His-tagged, or Flag-tagged transcription factors to double-stranded Agilent microarrays containing a DNA library designed to cover all possible 10-bp sequences, with every 8-mer occurring in at least 16 different spots on the array. This design allows comprehensive and unbiased characterization of the binding specificity of transcription factors for all possible 8-bp sequences.