Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data.

ABSTRACT: Efficient de novo motif discovery from the results of wide-genome mapping of transcription factor binding sites (ChIP-seq) is dependent on the choice of background nucleotide sequences. The foreground sequences (ChIP-seq peaks) represent not only specific motifs of target transcription factors, but also the motifs overrepresented throughout the genome, such as simple sequence repeats. We performed a massive comparison of the 'synthetic' and 'genomic' approaches to generate background sequences for de novo motif discovery. The 'synthetic' approach shuffled nucleotides in peaks, while in the 'genomic' approach selected sequences from the reference genome randomly or only from gene promoters according to the fraction of A/T nucleotides in each sequence. We compiled the benchmark

SUBMITTER: Raditsa VV 

PROVIDER: S-EPMC11282361 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature