Transcription factors (TFs) control the expression of genes through sequence-specific interactions with genomic DNA. Different TFs bind preferentially to different sequences, with the majority recognizing short (6-12 base), degenerate ‘motifs’. Modeling the sequence specificities of TFs is a central problem in understanding the function and evolution of the genome, because many types of genomic analyses involve scanning for potential TF binding sites. Models of TF binding specificity are also important for understanding the function and evolution of the TFs themselves. The challenge consists of predicting the signal intensities for the remaining TFs.
Evaluation of methods for modeling transcription factor sequence specificity
Weirauch, M. T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T. R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., Talukder, S., DREAM5 Consortium, Bussemaker H.J., Morris, Q.D., Bulyk, M.L., Stolovitsky G. and Hughes, T.R.
Nature Biotechnology 31, 126–134 (2013)
Link to Nature Biotechnology