SCIDDO

SCIDDO identifies differential chromatin domains (DCDs) from chromatin state segmentation maps to detect epigenetic regulatory changes and associate them with differential gene expression.

Key Features:

• Fast and Flexible Analysis: SCIDDO performs rapid differential analysis of chromatin state maps suitable for moderate computational resources.
• Statistical Rigor: SCIDDO employs a statistical framework to robustly identify differential chromatin domains.
• Integration with Chromatin State Maps: SCIDDO uses chromatin state segmentation maps that abstract co-occurring histone marks into discrete states.
• Correlation with Gene Expression Changes: SCIDDO identifies DCDs that correlate with changes in gene expression and aids recovery of differentially expressed genes (DEGs).
• Interrogation of Chromatin Dynamics: SCIDDO can directly analyze chromatin dynamics, including enhancer switches.
• Stable Performance Across Comparisons: SCIDDO maintains stable identification of DEGs across cell-type comparisons and parameter cut-offs.

Scientific Applications:

• Detection of Differential Chromatin Domains: Identifying DCDs across samples or conditions using chromatin state segmentation maps.
• Linking Epigenetic Changes to Gene Expression: Correlating DCDs with differential gene expression to recover DEGs.
• Analysis of Regulatory Element Dynamics: Investigating enhancer switches and other chromatin dynamics underlying regulatory element activity.

Methodology:

Processes chromatin state segmentation maps derived from genome-wide histone modification data obtained through chromatin immunoprecipitation sequencing (ChIP-seq), abstracts individual histone marks into chromatin state segmentation maps, and applies a statistical framework to identify reproducible differential chromatin domains.