Factorbook

Factorbook catalogs transcription factor (TF) motifs and candidate regulatory motif sites and provides annotations and integrative analyses derived from ENCODE Phase II and III ChIP-seq and HT-SELEX data to support studies of TF binding and gene regulation.

Key Features:

• Data sources: Derived from ENCODE Phase II ChIP-seq profiling of approximately 1,600 DNA-binding transcription factors and expanded with thousands of additional ENCODE Phase II and III ChIP-seq experiments and HT-SELEX data.
• Expanded motif catalog: Integrates experimental datasets to provide a comprehensive collection of TF binding motifs.
• ENCODE registry integration: Links motifs to the ENCODE registry of candidate cis-regulatory elements for genome-wide annotation of candidate TF binding sites.
• Machine learning tools: Provides motif models that can be applied within machine learning frameworks for integrative analyses.
• Variant annotation and heritability assessment: Enables annotation of genetic variants and assessment of their association with disease and trait heritability using motif-based analyses.

Scientific Applications:

• Gene regulation studies: Characterizes TF binding specificities and motif occurrences to inform regulatory mechanism analyses.
• Variant interpretation: Annotates genetic variants in regulatory motifs to investigate potential functional impacts on TF binding.
• Disease and trait heritability analyses: Assesses contributions of TF motifs to disease associations and trait heritability.
• Genome-wide TF binding annotation: Maps candidate TF binding sites across cell types by linking motifs to candidate cis-regulatory elements.

Methodology:

Uses ENCODE Phase II and III ChIP-seq and HT-SELEX experimental data to derive TF motifs, integrates motifs with the ENCODE registry of candidate cis-regulatory elements, and provides motif models for application in machine learning frameworks to enable variant annotation and heritability analyses.