Cistrome

Cistrome analyzes ChIP-chip and ChIP-seq data to enable integrative and reproducible analyses in genomics and epigenetics.

Key Features:

• Comprehensive toolset: Includes 29 specialized tools tailored for ChIP-chip and ChIP-seq analyses, organized into functional categories.
• Preliminary peak calling and correlation analyses: Performs identification of DNA binding regions (peaks) and assesses correlations within datasets.
• Downstream genome feature association: Associates identified peaks with genomic features to characterize regulatory contexts.
• Gene expression analyses: Integrates ChIP-chip/ChIP-seq data with gene expression data for combined analysis.
• Motif discovery: Performs sequence motif discovery within identified peaks to identify potential binding sites.

Scientific Applications:

• Functional genomics: Supports studies that link protein-DNA interactions to genomic function and regulation.
• Transcription factor and DNA-binding protein analysis: Aids in elucidating binding locations and roles of transcription factors and other DNA-binding proteins.
• Gene regulatory network inference: Facilitates integration of ChIP-chip/ChIP-seq and gene expression data to investigate gene regulation networks.
• Regulatory element discovery: Uses motif discovery within peaks to identify novel regulatory elements and potential binding motifs.

Methodology:

Built on the Galaxy framework and implemented with standardized workflows to support reproducible ChIP-chip and ChIP-seq analyses.