ReMoDiscovery

ReMoDiscovery infers transcriptional module networks by integrating ChIP-chip data, DNA motif information, and gene expression profiles to correlate regulatory programs with their regulators and motifs for sets of co-expressed genes.

Key Features:

• Concurrent Data Integration: Integrates ChIP-chip, motif information, and gene expression profiles concurrently to inform network inference.
• Correlation of Regulatory Programs and Regulators: Correlates regulatory programs with corresponding transcriptional regulators and DNA-binding motifs based on co-expression patterns.
• ChIP-chip and Motif Evidence: Leverages ChIP-chip data to identify protein–DNA interactions and motif information to recognize binding sites.
• Transcriptional Module Inference: Infers modules of co-expressed genes and associates them with regulatory programs to construct transcriptional module networks.
• Speed and Tunability: Provides rapid processing capabilities and adjustable algorithmic parameters for tuning analyses.

Scientific Applications:

• Yeast transcriptional network analysis: Applied to yeast data to confirm known regulatory relationships and to predict potential novel regulatory roles.

Methodology:

Systematically correlates regulatory programs with their transcriptional regulators and motifs using co-expression patterns across integrated ChIP-chip, motif, and gene expression datasets, leveraging ChIP-chip to identify protein–DNA interactions, motif data to recognize binding sites, and expression profiles to define co-expressed gene sets for constructing transcriptional module networks.