Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.

ABSTRACT: Gene regulatory networks are ultimately encoded by the sequence-specific binding of (TFs) to short DNA segments. Although it is customary to represent the binding specificity of a TF by a position-specific weight matrix (PSWM), which assumes each position within a site contributes independently to the overall binding affinity, evidence has been accumulating that there can be significant dependencies between positions. Unfortunately, methodological challenges have so far hindered the development of a practical and generally-accepted extension of the PSWM model. On the one hand, simple models that only consider dependencies between nearest-neighbor positions are easy to use in practice, but fail to account for the distal dependencies that are observed in the data. On the other hand, models t

SUBMITTER: Omidi S 

PROVIDER: S-EPMC5550003 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature