Figure 1
From: Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data
DE Novo motIf diScovery (DENIS) framework. (a) The framework receives continuous binding scores as minimal input. In the first step, the binding scores are scanned and footprints (FPs) are extracted genome-wide. If binding scores for two conditions are provided as input, differential binding will be assessed. (b) Sequences at detected FPs are extracted and used to perform data driven de novo motif prediction. In an iterative process, most prominent motifs are extracted and corresponding sequences are removed from the motif discovery pool. FPs not (yet) used are kept for following discovery runs. (c) Resulting motifs are subjected to downstream analysis. DENIS provides (1) an individual motif site annotation module (e.g. annotation to genes)11, (2) a motif database comparison module, (3) a module to compute global binding site enrichment in open chromatin, and (4) based on the annotation module, a motif based gene set enrichment analysis (GSEA) module12. All subfigures were created with BioRender.com.
