Cscan

Cscan analyzes genome-wide Chromatin Immunoprecipitation Sequencing (ChIP-Seq) data to identify transcription factors (TFs), histone modifications, RNA polymerase binding and other epigenetic markers associated with user-specified gene loci to elucidate transcriptional regulatory mechanisms.

Key Features:

• Extensive ChIP-Seq dataset collection: Hosts a repository of genome-wide ChIP-Seq experiments covering transcription factors (TFs), histone modifications, RNA polymerases and other epigenetic markers.
• Integration with genomic coordinates: Cross-references enriched ChIP-Seq peak regions with the genomic coordinates of input genes to detect overlaps.
• Input flexibility: Accepts clusters of co-expressed genes or arbitrary gene sets as input for regulatory analysis.
• Identification of common regulators: Detects TFs likely to be common regulators of input genes by analyzing peak–gene overlaps and reporting correlations among regulators.
• Investigation of gene regulation dynamics: Enables analysis of promoter activation, transcriptional activity, histone modification patterns, and RNA polymerase binding at gene loci.
• Cell/tissue specificity analysis: Allows interrogation of cell- or tissue-specific ChIP-Seq signals to contextualize regulatory interactions.

Scientific Applications:

• Regulatory element and TF identification: Identifying key transcription factors and regulatory elements associated with specific gene sets.
• Epigenetic modification analysis: Exploring histone modifications and other epigenetic marks and their relationships to gene expression.
• Tissue- or condition-specific regulation studies: Investigating cell- or tissue-specific and condition-specific patterns of gene regulation.
• Hypothesis generation for genomic function: Facilitating generation of hypotheses about the functional roles of genomic regions based on ChIP-Seq signal overlap.

Methodology:

Integration of ChIP-Seq enriched peak regions with genomic coordinates of input genes followed by statistical analysis to identify significant overlaps.