TFBScluster

TFBScluster identifies conserved transcription factor binding site (TFBS) clusters across mammalian genomes to support reconstruction of transcriptional regulatory networks from gene expression profiling data.

Key Features:

• Genome-wide identification: Performs genome-wide searches to identify clusters of TFBSs conserved across mammalian species, including human and mouse.
• Genome browser integration: Links search results to ENSEMBL and UCSC genome browsers to provide genomic context for identified clusters.
• Annotation and expression integration: Integrates TFBS searches with genome annotation and gene expression profiling data to prioritize computational predictions for experimental validation.
• Customizable search parameters: Allows filtering of clusters by additional DNA sequence motifs and by constraints on binding site orientation or order.
• Detailed results files: Generates detailed results files to support experimental validation of predicted regulatory elements.

Scientific Applications:

• Transcriptional regulatory network reconstruction: Supports reconstruction of transcriptional regulatory networks from gene expression profiling datasets using conserved TFBS cluster locations.
• Functional annotation of non-coding regions: Enables annotation of non-coding genomic regions by identifying conserved regulatory sequences.
• Study of developmental regulation: Identifies conserved TFBS clusters that may regulate mammalian developmental processes.

Methodology:

Integrates multiple computational tools and leverages conservation across mammalian genomes for genome-wide identification and characterization of conserved TFBS clusters.