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Gene transcription is controlled through an enormous diversity of regulatory factors, which often play a key role in enabling or disabling particular cellular programs. Most common among these factors are a variety of proteins that bind to DNA and regulate gene expression (transcription factors), comprise the structure of chromatin (nucleosomes), or chemical modifications to chromatin (histone modifications, DNA methylation). The CRI provides analysis support for numerous epigenomic experiments, including:

  • ChIP-seq of transcription factors or histone modifications
  • Measurements of open chromatin via ATAC-seq, DNAase-seq, or FAIRE-seq
  • DNA methylation via MeDIP or Bisulfite sequencing

Analysis of these data sets typically includes steps like peak calling, and creation of enrichment tracks (bigWig files), in addition to raw data quality control and genome alignment. We provide numerous additional analyses as well, such as de novo motif detection, motif enrichment analysis, annotation of proximal and distal genes, and integration of peaks with gene expression data (from RNA-seq or microarray) for inference of regulatory effects.