MYBS

MYBS maps transcription factors and their binding sites by integrating ChIP-chip data and predicted position weight matrices (PWMs) to identify TFBSs in yeast promoters.

Key Features:

• Integration of experimental and predictive data: Combines ChIP-chip experimental evidence with predicted PWMs to support TFBS identification.
• Phylogenetic footprinting filter: Uses phylogenetic footprinting as a filter to prioritize evolutionarily conserved binding sites.
• Motif and gene queries: Supports motif-based and gene-based searches to locate motif occurrences within gene promoters.
• Motif database compilation: Maintains 481 consensus sequences and 71 PWMs corresponding to 183 transcription factors compiled from eleven distinct databases.
• Parallel regulator analysis: Provides analysis to examine potential regulators in parallel for a given set of genes.
• TF pair target identification: Identifies target gene sets associated with TF pairs to investigate combinatorial regulation.

Scientific Applications:

• TF and TFBS mapping: Mapping transcription factors and their binding sites within yeast promoters using combined experimental and predictive evidence.
• Conserved site discovery: Identifying evolutionarily conserved TFBSs via phylogenetic footprinting to prioritize functional sites.
• Promoter motif analysis: Detecting motif occurrences in promoters for hypothesis generation about regulatory elements.
• Combinatorial regulation analysis: Inferring regulatory associations and target gene sets for TF pairs to study combinatorial control.

Methodology:

Integrates ChIP-chip data with PWM-based motif scanning and consensus sequences, applies phylogenetic footprinting as a conservation filter, and relies on a compiled database of 481 consensus motifs and 71 PWMs for 183 TFs from eleven databases.