ChIP-seq data analysis in Genome Enhancer

ChIP-seq data analysis in Genome Enhancer

Genome Enhancer is a fully automatized pipeline for analyzing patient omics data and studying the molecular mechanism underlying the observed pathology. Genome Enhancer identifies prospective drug targets and associated treatments from the input omics data, supported data formats include ChIP-seq data.


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We provide a number of demo reports demonstrating how Genome Enhancer results would look like on various inputs. Full list of all available demo reports can be found here. Below you will find the demo report that demonstrates the results of Genome Enhancer analysis ran on the ChIP-seq data.


Demo report ‘Cetuximab resistant cells in oral cancer (GSE205455) — Epigenomics, BED’ – demonstrating how BED files can be analyzed in Genome Enhancer:
Other Genome Enhancer demo reports, which provide examples of Genome Enhancer outputs on other input omics data types, can be found here.
How does it work
Genome Enhancer uses Upstream Analysis, an integrated promoter and pathway analysis, to identify potential drug targets of the studied pathology.

In the first step of this analysis the transcription factors that regulate the genes with the highest number of ChIP-seq peaks are identified with the use of the TRANSFAC® database of transcription factors binding sites.

The second step searches for common master-regulators of the identified transcription factors by building a personalized signal transduction network of the studied pathology using the TRANSPATH®   database of  mammalian signal transduction and metabolic pathways.

The identified master regulators are prospective drug target candidates. They are used for further selection of chemical compounds that can bring therapeutic benefit for the studied clinical case. In this step the HumanPSD database is employed to identify drugs that have been tested in clinical trials. The cheminformatic tool PASS predicts small molecules that can affect the identified targets.

Finally, Genome Enhancer generates a comprehensive analysis report about the personalized drug targets identified for a certain patient, or a group of patients, and the drugs that may be effective in this case. You can view a number of Genome Enhancer demo reports here.

A detailed description of full Genome Enhancer analysis schema, including all steps of epigenomics data pre-processing, which are performed by the system for finding the genes with the highest number of ChIP-seq peaks mapped to them, can be found on this page. Epigenomics data can be loaded to Genome Enhancer in one of the following formats:

Epigenomics (ChIP-seq) supported input formats:

  • *.fastq
  • *.bam (hg38 only)
  • *.bed (hg38 only)
  • Table data with Illumina methylation probe ids, cg*

You are welcome to purchase a paid subscription for Genome Enhancer by requesting it here.

For further info please explore the Genome Enhancer product page.

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