The jigsaw puzzle of sequence phenotype inference: Piecing together Shannon entropy, importance sampling, and Empirical Bayes

Abstract: A nucleotide sequence 35 base pairs long can take 1,180,591,620,717,411,303,424 possible values. An example of systems biology datasets, protein binding microarrays, contain activity data from about 40000 such sequences. The discrepancy between the number of possible configurations and the available activities is enormous. Thus, albeit that systems biology datasets are large in absolute terms, they oftentimes require methods developed for rare events due to the combinatorial increase in the number of possible configurations of biological systems. A plethora of techniques for handling large datasets, such as Empirical Bayes, or rare events, such as importance sampling, have been developed in the literature, but these cannot always be simultaneously utilized. Here we introduce a principled approach to Empirical Bayes based on importance sampling, information theory, and theoretical physics in the general context of sequence phenotype model induction. We present the analytical calculations that underlie our approach. We demonstrate the computational efficiency of the approach on concrete examples, and demonstrate its efficacy by applying the theory to publicly available protein binding microarray transcription factor datasets and to data on synthetic cAMP-regulated enhancer sequences. As further demonstrations, we find transcription factor binding motifs, predict the activity of new sequences and extract the locations of transcription factor binding sites. In summary, we present a novel method that is efficient (requiring minimal computational time and reasonable amounts of memory), has high predictive power that is comparable with that of models with hundreds of parameters, and has a limited number of optimized parameters, proportional to the sequence length.