Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses.

ABSTRACT: A high-confidence map of the direct, functional targets of each transcription factor (TF) requires convergent evidence from independent sources. Two significant sources of evidence are TF binding locations and the transcriptional responses to direct TF perturbations. Systematic data sets of both types exist for yeast and human, but they rarely converge on a common set of direct, functional targets for a TF. Even the few genes that are both bound and responsive may not be direct functional targets. Our analysis shows that when there are many nonfunctional binding sites and many indirect targets, nonfunctional sites are expected to occur in the cis-regulatory DNA of indirect targets by chance. To address this problem, we introduce dual threshold optimization (DTO), a new method for se

SUBMITTER: Kang Y 

PROVIDER: S-EPMC7111528 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature