Condition-specific binding preferences are an important biological property of certain TFs [45]. Polymorphisms and de novo mutations may also alter a sequence of a particular binding site complicating known-TFBS discovery [46], [47]. Hence, we reasoned that certain ab initio MFs might reflect condition-driven, or protein complex-dependent, deviations from known TFBS models. We therefore compared the ab initio identified MFs to those already associated with known TFs. We confirmed five models and added one new TFBS model (NKX3-2) to our roster of lncRNA-promoter-enriched TFBSs (Table S2, Figure S2e–f).
