MotifViz

MotifViz identifies overrepresented transcription factor binding motifs within promoter sequences of co-regulated genes to aid elucidation of transcriptional regulatory mechanisms.

Key Features:

• Integrated motif discovery: Combines the motif discovery programs Clover, Rover, Motifish, and Possum to provide multiple analytical capabilities.
• Diverse algorithmic approaches: Leverages the distinct algorithms of Clover, Rover, and Motifish to offer complementary perspectives on motif identification.
• Motif matching and validation: Uses Possum as a motif-matching program for basic comparisons and validation of findings from discovery algorithms.
• Promoter-focused analysis: Targets promoter sequences of co-regulated genes to detect overrepresented transcription factor binding sites.

Scientific Applications:

• Transcription factor binding site identification: Detects motifs that are overrepresented among sets of co-regulated genes to suggest candidate transcription factor binding sites.
• Regulatory network inference: Supports the identification of shared regulatory motifs that can inform reconstruction of transcriptional regulatory networks and coordinated gene control.
• Support for genomics and systems biology: Provides motif-level insights applicable to genomics, molecular biology, and systems biology investigations of gene regulation.

Methodology:

Integrates Clover, Rover, Motifish, and Possum to scan promoter sequences and identify overrepresented transcription factor binding motifs using each program's distinct algorithms.