spatzie

spatzie analyzes transcription factor motif co-enrichment in enhancer-promoter interactions to characterize cooperative transcription factor behavior underlying genome organization and gene regulation.

Key Features:

• R package implementation: Provided as an R package for performing analyses of transcription factor motif co-enrichment in genomic interaction data.
• Statistical tests for motif co-enrichment: Implements robust statistical methodologies to detect significant co-enrichment of transcription factor motifs within enhancer-promoter interactions.
• Validation with simulated ChIP-seq data: Validated using controlled experiments with simulated data derived from ChIP-seq to assess detection of co-enriched motifs in noisy datasets.
• Application to ChIA-PET data: Applied to human ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) data to investigate cell type-specific transcription factor cooperativity.

Scientific Applications:

• Analysis of TF cooperativity at enhancer-promoter interfaces: Enables exploration of how transcription factors cooperate at enhancer-promoter interfaces to influence gene regulation.
• Investigation of genome organization and gene regulation: Facilitates studies into mechanisms of genome organization and regulation across different cell types.
• Study of transcriptional networks and disease: Supports analysis of transcriptional network interactions and their roles in cellular function and disease.

Methodology:

Implements statistical tests for detecting transcription factor motif co-enrichment in enhancer-promoter interactions, validated with simulated data derived from ChIP-seq, and applied to human ChIA-PET datasets to assess cell type-specific cooperativity.