TOUCAN 2

TOUCAN 2 identifies cis-regulatory elements in metazoan genomic sequences to support discovery and analysis of transcription factor binding sites and comparative detection of cis-regulatory modules.

Key Features:

• Database integration and retrieval: Automatically fetches genes, intergenic regions, and orthologous sequences from Ensembl and EMBL.
• Putative regulatory region identification: Aligns orthologs and selects syntenic regions to define candidate regulatory regions.
• MotifScanner (known TFBS scoring): Scores position weight matrices using a probabilistic model to detect known transcription factor binding sites.
• MotifSampler (de novo motif discovery): Identifies candidate motifs corresponding to unknown transcription factors using Gibbs sampling.
• Statistical over-representation analysis: Applies a binomial test to identify binding sites over-represented in a gene set versus a reference sequence set.
• Comparative genomics and cis-regulatory module detection: Implements comparative genomics approaches for detection of cis-regulatory modules across orthologous sequences.

Scientific Applications:

• Known TFBS detection in intergenic DNA: Detects established transcription factor binding sites within intergenic regions.
• Discovery of candidate sites for unknown TFs: Identifies biologically plausible novel motifs for unknown transcription factors.
• Gene-set regulatory analysis: Applied to muscle-specific genes, liver-specific genes, and E2F target genes to validate detection of regulatory elements.
• Hypothesis generation for gene regulation: Supports formulation of testable hypotheses about regulation of individual genes or co-regulated gene sets.

Methodology:

Fetch genes and intergenic regions including orthologs from Ensembl or EMBL; align orthologs and select syntenic regions; score position weight matrices with MotifScanner using a probabilistic model; discover motifs with MotifSampler using Gibbs sampling; apply a binomial test for over-representation; employ comparative genomics methods for cis-regulatory module detection.