The cis-trans binding strength defined by motif frequencies facilitates statistical inference of transcriptional regulation.

ABSTRACT:

Background

A key problem in systems biology is the determination of the regulatory mechanism corresponding to a phenotype. An empirical approach in this regard is to compare the expression profiles of cells under two conditions or tissues from two phenotypes and to unravel the underlying transcriptional regulation. We have proposed the method BASE to statistically infer the effective regulatory factors that are responsible for the gene expression differentiation with the help from the binding data between factors and genes. Usually the protein-DNA binding data are obtained by ChIP-seq experiments, which could be costly and are condition-specific.

Results

Here we report a definition of binding strength based on a probability model. Using this condition-free definition, the BA

SUBMITTER: Feng Y 

PROVIDER: S-EPMC6509875 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature