Background: The fundamental step of leaming transcriptional regulation mechanism is to identify the target genes regulated by transcription factors (TFs).Despite numerous target genes identified by Chromatin immunoprecipitation followed by high-throughput sequencing technology (ChIP-seq) assays, it is not possible to infer function from binding alone in vivo.This is equally true in one of the best model systems, the nematode Caenorhabditiselegans (C.elegans), where regulation often occurs through diverse TFs binding features of transcriptional networks identified in modENCODE.