BindCompare

BindCompare analyzes protein-nucleic acid binding datasets to identify combinatorial associations between transcription factors and RNA binding proteins, generating testable hypotheses about their co-regulation of target genes.

Key Features:

• Cross-factor binding analysis: Compares and contrasts interactions of multiple transcription factors and RNA binding proteins with nucleic acids to identify common and unique targets.
• Organism-agnostic analysis: Analyzes data from any organism with known annotated genome information.
• Genomic output generation: Outputs files with detailed genomic locations and gene information for targets to support downstream analysis.
• Co-binding identification: Identifies transcription factors and RNA binding proteins that co-bind to the same DNA and/or RNA loci.

Scientific Applications:

• Gene regulatory network modeling: Supports the identification of testable gene regulatory network models governed by combinatorial associations between factors.
• Combinatorial regulation hypothesis generation: Generates testable hypotheses about combinatorial regulation of target genes by co-binding transcription factors and RNA binding proteins.

Methodology:

The sources do not explicitly detail the computational steps or algorithms used.