Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.

ABSTRACT: Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) is a central genome-wide method for in vivo analyses of DNA-protein interactions in various cellular conditions. Numerous studies have demonstrated the complex contextual organization of ChIP-seq peak sequences and the presence of binding sites for transcription factors in them. We assessed the dependence of the ChIP-seq peak score on the presence of different contextual signals in the peak sequences by analyzing these sequences from several ChIP-seq experiments using our fully enumerative GPU-based de novo motif discovery method, Argo_CUDA. Analysis revealed sets of significant IUPAC motifs corresponding to the binding sites of the target and partner transcription factors. For these ChIP-seq experiments

SUBMITTER: Vishnevsky OV 

PROVIDER: S-EPMC10816497 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature