HOCOMOCO

HOCOMOCO provides a comprehensive collection of DNA-binding specificity models for human and mouse transcription factors to support analysis of transcriptional regulation.

Key Features:

• Extensive database: HOCOMOCO v11 contains 680 human and 453 mouse transcription factor binding models represented as position weight matrices (PWMs).
• Mononucleotide and dinucleotide models: The collection includes 1,302 mononucleotide PWMs and 576 dinucleotide PWMs to capture primary and alternative binding specificities.
• Data-driven updates from ChIP-Seq: Models were derived and refined using data from over five thousand ChIP-Seq experiments, replacing models based solely on in vitro data.
• Processing and aggregation: ChIP-Seq experiments were processed within the BioUML framework and aggregated in the Genome Transcription Regulation Database (GTRD).
• Complementary motif tools: MoLoTool (Motif Location Toolbox) uses HOCOMOCO models to visualize predicted binding sites in short DNA sequences.

Scientific Applications:

• Transcriptional regulation studies: Use HOCOMOCO PWMs to investigate transcription factor binding preferences and their role in gene regulation.
• Genomic annotation and analysis: Annotate genomic sequences with potential transcription factor binding sites for functional genomics analyses.
• Comparative genomics: Compare human and mouse transcription factor binding models to support cross-species regulatory and evolutionary studies.

Methodology:

Systematic motif discovery from over five thousand ChIP-Seq experiments processed uniformly within BioUML using multiple peak-calling tools and aggregated in GTRD.