Imetagene

Imetagene performs metagene analysis to integrate, summarize, and compare ChIP-Seq enrichment signals from complex experimental designs.

Key Features:

• Integration with metagene and similaRpeak: Interoperates with the metagene package to aggregate ChIP-Seq enrichment into metagene plots and with similaRpeak to assess similarities and dissimilarities among ChIP-Seq profiles.
• Aggregation into metagene plots: Aggregates ChIP-Seq enrichment signals across genomic regions to produce metagene summaries.
• Profile comparison: Identifies similarities and dissimilarities across large numbers of ChIP-Seq profiles using similaRpeak.
• Support for complex experimental designs: Integrates and summarizes ChIP-Seq data from multifactorial experimental layouts for comparative analysis.

Scientific Applications:

• Regulatory factor occupancy at promoters and enhancers: Investigates differential occupancy of regulatory factors at noncoding regulatory regions such as promoters and enhancers.
• Correlation with transcriptional activity: Explores correlations between transcriptional activity and regulatory factor occupancy, exemplified in GM12878 B-lymphocytes.
• Detection of gradient and threshold effects: Reveals gradient effects where occupancy follows transcription patterns and threshold effects where occupancy saturates before maximal transcription.

Methodology:

Implemented in R; aggregates ChIP-Seq enrichment signals into metagene plots via the metagene package; assesses similarities and dissimilarities among ChIP-Seq profiles using similaRpeak; integrates, summarizes, and compares ChIP-Seq enrichment from complex experimental designs.