Genome Enhancer


 Welcome to the new era of Precision Medicine

Meet Genome Enhancer – a fully automated pipeline for patient omics data analysis, which identifies prospective drug targets and corresponding treatments by reconstructing the molecular mechanism of the studied pathology.

You can login to Genome Enhancer directly with your geneXplain® platform account or register for a new account in just several seconds to check out this great tool yourself.

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 differentially expressed or mutated genes 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 at the corresponding section of this page.

 

You are welcome to activate a free trial or purchase a paid subscription for Genome Enhancer at the geneXplain store.

Key features

  • Identifies activated targets in the examined patient data and suggests known and re-purposing drugs
  • Based on well accepted databases TRANSFAC®, TRANSPATH®, HumanPSD™
  • Applies unique in-house developed algorithms
  • Suites for use by researches and by medical doctors
  • Does not require special skills to operate
  • Analyses all types of omics data starting either with raw or pre-processed data
  • Generates a comprehensive report on the identified drug targets and prospective therapies

Only three steps to launch the analysis


 

Running Genome Enhancer takes only three steps:

1. Upload your data to the server and specify the import options (data type)


2. Split your data by the conditions you want to compare


3. Launch the analysis by specifying the conditions to be compared and the disease and tissue types (optional)

The analysis report will be ready shortly. Depending on your input data, it will include lists of differentially expressed or mutated genes; transcription factors, regulating those genes; reconstructed signaling network of the studied pathological process; potential drug targets and corresponding known drugs and re-purposing drugs, which may be effective in the studied case, as well as further cheminformatically predicted drug-like compounds. The report also contains description of analysis methods used and the references.

Acceptable input data formats

Genome Enhancer works with genomics, transcriptomics, epigenomics, proteomics and metabolomics input data types of the following formats:

Transcriptomics (RNA-seq, microarrays)

*.txt, *.csv, *.xls (table with gene identifiers)

*.CEL (affymetrix)

*.txt (special agilent format)

*.txt (special illumina format)

*.fastq

Epigenomics (ChIP-seq)

*.fastq

*.bam (hg38 only)

*.bed (hg38 only)

*.txt (table with illumina methylation probe ids, cg*)

Genomics

*.vcf

*.txt, *.csv, *.xls (table data with SNP identifiers, rs*)

*.fastq

Proteomics

*.txt, *.csv, *.xls (table with protein identifiers)

Metabolomics

*.txt, *.csv, *.xls (table with the list of metabolites from chebi database, e.g. CHEBI:57316)


Files of one data format can be uploaded in a .zip archive

What we offer

Multi-omics analysis

Use genomics, transcriptomics, metabolomics, proteomics, and epigenomics data in one analysis run and receive an integrated report

 

Easy interface

Due to complete automation of the analysis, the system can be used by medical doctors and biologists without any bioinformatics skills

 

Personalized medicine

Running the analysis on omics data of a certain patient, you will identify personalized prospective drug targets and corresponding treatments

 

Scientific base

Integration of promoter and enhancer analysis with pathway reconstruction gives unrivaled disease molecular mechanism modeling accuracy

Drug target identification

Genome Enhancer reconstructs a complex network of signal transduction pathways that are activated in the pathology and identifies their key regulators

 

 

Flexible pricing

Select the license which fits you best – both short-term and long-term licenses are supported by our flexible tariffs. For more details visit the geneXplain store

Report examples

You can view various analysis report examples generated by Genome Enhancer on the basis of different omics input data types and various origins of the studied pathologies:

References

  1. Kel, Alexander, et al. “Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer.” BMC bioinformatics 20.4 (2019): 119.
  2. Kolpakov, Fedor, et al. “BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data.” Nucleic acids research 47.W1 (2019): W225-W233.
  3. Boyarskikh, Ulyana, et al. “Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3.” BMC medical genomics 11.1 (2018): 12.
  4. Boyarskikh, U. A., et al. “Master-regulators driving resistance of non-small cell lung cancer cells to p53 reactivator Nutlin-3.” Virtual Biology 4 (2017): 1-31.
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