known-motif-enrichment

Known motif enrichment on ATAC-seq or ChIP-seq peaks identifies transcription factor motifs by comparing peak regions against established databases using HOMER. You provide BED, narrowPeak, broadPeak, or gene lists to generate motif tables, logos, and logs.

HOMER motif enrichment analysis accepts BED, narrowPeak, broadPeak, and gene lists as input formats. Gene lists enable promoter-focused motif analysis, while peak files facilitate direct detection of known transcription factor motif enrichments in genomic regions.

You can use a gene list for known motif enrichment to perform promoter-focused analysis. HOMER analyzes promoter regions associated with the provided genes to identify enriched known transcription factor motifs from established databases.

HOMER known motif enrichment generates a project directory containing homerResults, logs, and parameter files. These outputs include motif tables, motif logos, and detailed logs to ensure comprehensive reproducibility of the transcription factor enrichment analysis.

HOMER motif enrichment supports optional genome specification for analyzing custom datasets. This allows the enrichment workflow to correctly map BED, narrowPeak, broadPeak, or gene list inputs against the appropriate genomic reference during known motif detection.

Known motif enrichment compares ChIP-seq peaks against established transcription factor databases, providing direct identification of driving TFs. This approach offers faster, targeted results compared to open-ended discovery when seeking known regulatory motifs.