TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information.

ABSTRACT: A gene regulatory network (GRN) is a collection of regulatory interactions between transcription factors (TFs) and their target genes. GRNs control different biological processes and have been instrumental to understand the organization and complexity of gene regulation. Although various experimental methods have been used to map GRNs in Arabidopsis thaliana, their limited throughput combined with the large number of TFs makes that for many genes our knowledge about regulating TFs is incomplete. We introduce TF2Network, a tool that exploits the vast amount of TF binding site information and enables the delineation of GRNs by detecting potential regulators for a set of co-expressed or functionally related genes. Validation using two experimental benchmarks reveals that TF2Network predicts t

SUBMITTER: Kulkarni SR 

PROVIDER: S-EPMC5888541 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature