Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data.

ABSTRACT:

Background

Transcription factors (TFs) bind to DNA in a highly sequence-specific manner. This specificity manifests itself in vivo as differences in TF occupancy between the two alleles at heterozygous loci. Genome-scale assays such as ChIP-seq currently are limited in their power to detect allele-specific binding (ASB) both in terms of read coverage and representation of individual variants in the cell lines used. This makes prediction of allelic differences in TF binding from sequence alone desirable, provided that the reliability of such predictions can be quantitatively assessed.

Results

We here propose methods for benchmarking sequence-to-affinity models for TF binding in terms of their ability to predict allelic imbalances in ChIP-seq counts. We use a likelihood functi

SUBMITTER: Li X 

PROVIDER: S-EPMC11529166 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature