COUGER

COUGER identifies putative protein co-factors that distinguish the genomic binding profiles of paralogous transcription factors to explain differential in vivo specificity.

Key Features:

• Paralogous TF focus: Targets paralogous transcription factors (TFs) that share DNA binding domains and similar DNA binding preferences but exhibit distinct in vivo specificities.
• Comparative region analysis: Analyzes two sets of genomic regions bound by the respective TFs to detect distinguishing signals.
• Co-factor identification: Pinpoints a small set of putative protein co-factors that best distinguish the binding profiles of the two TFs.
• Classification-based framework: Employs a classification-based framework to discriminate between the binding profiles of the paralogous TFs.
• DNA-binding specificity features: Utilizes features reflective of the DNA-binding specificities of potential co-factors.
• Feature contribution analysis: Assesses the contributions of individual co-factor features to the discrimination between TF binding profiles.

Scientific Applications:

• Paralogous TF specificity elucidation: Identify co-factors mediating differential regulatory roles among paralogous TFs.
• Transcriptional regulation studies: Investigate mechanisms underlying TF binding specificity and transcriptional regulation.
• Gene expression and epigenetics: Explore how co-factors influence gene expression regulation and epigenetic contexts.
• Comparative genomic binding analysis: Compare genomic binding profiles to infer co-factor-driven specificity between related TFs.

Methodology:

Compares two TF-bound genomic region sets using a classification-based framework with features derived from DNA-binding specificities to select a small discriminative set of putative co-factors and assess individual feature contributions.