Using Partek to Analyze ChIP-Seq Data

The HSLS Molecular Biology Information Service (HSLS-MBIS) provides access to many bioinformatics analysis tools, including Partek Flow. University of Pittsburgh researchers are now able to perform chromatin immunoprecipitation sequencing (ChIP-Seq) analysis using Partek software to determine how proteins interact with DNA and regulate gene expression.

ChIP-Seq uses high-throughput DNA sequencing to map protein-DNA interactions across the entire genome. The point-and-click user interface in Partek software helps researchers to quickly build a start-to-finish ChIP-Seq pipeline and:

  • identify enriched genomic regions
  • filter and annotate genomic regions
  • detect known motifs
  • discover novel motifs
  • visualize enriched genomic regions and motifs
  • find enriched gene sets
  • integrate with gene expression data

Partek software allows for the easy integration of ChIP-Seq and RNA-Seq studies into a single study. First, peaks and transcription factor binding sites are identified in the ChIP-Seq data, then the peaks are annotated to the genome to locate the nearest transcription start site. Next, a targeted gene list generated from the ChIP-Seq data is compared to a list of differentially expressed genes from RNA-Seq data, followed by visualization using a Venn diagram. The Partek chromosome view allows for the combined visualization of peaks and differentially expressed genes. A webinar describing this process is available.

View full image:

Anyone with a University of Pittsburgh e-mail address can register for access to Partek software via the HSLS license. For more information, contact the HSLS Molecular Biology Information Service.

*Parts of this article content were derived from the Partek ChIP-Seq website.

~Carrie Iwema