Genome Enhancer

Genome Enhancer





Release 3.3 is now out!


 


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. Proven applications of Genome Enhancer include cancer, neurodegenerative diseases, infectious diseases, diabetes and metabolic diseases, hypertension.




Genome Enhancer is also available as a part of TRANSFAC full package – a powerful synergism between the automatic pipeline for multi-omics data processing of Genome Enhancer and the comprehensive bioinformatics toolbox of the geneXplain® platform integrated with TRANSFAC, TRANSPATH, and HumanPSD databases. Find details on the TRANSFAC full package here.


 


Request Genome Enhancer price info


 




 




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.








 


A detailed description of Genome Enhancer analysis schema can be found on this page.


Check out the Genome Enhancer video channel ran by the CSO of geneXplain GmbH Dr. Alexander Kel. See how various omics data can be analyzed in Genome Enhancer or even send your own data to Dr. Kel and he will show its analysis in one of the next videos!




                                            

                                                                            
                                                           
                                                           

                                        
                        

                                                                        


   
    
Key features

    
    

  • Identifies activated targets in the examined patient data and suggests known and re-purposing drugs
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  • Based on well accepted databases TRANSFAC®, TRANSPATH®, HumanPSD™
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  • Applies unique in-house developed algorithms
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  • Suites for use by researches and by medical doctors
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  • Does not require special skills to operate
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  • Analyses all types of omics data starting either with raw or pre-processed data
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  • Generates a comprehensive report on the identified drug targets and prospective therapies
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  • Generates MTB (Molecular Tumor Board) report on patient’s genomics data for a number of pathologies (if not more than 2 conditions were selected during the analysis launch)
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In addition to that, all our customers enjoy the following advantages or our products:






–       Technical and scientific support or your research: rapid answers to your questions from our professional support team will be always provided






–       Secure cloud space connected with online licenses that can be accessed from any location






–       Extensive manuals, documentation, examples, and tutorials available for all our products






–       Frequent releases and updates of our databases contents and software functionality






–       Ability to request personal training sessions


–       All our servers are running on CO2-neutral water or wind power


 




Available solutions


Genome Enhancer can be licensed independently or as an integrative part of the TRANSFAC full package providing a powerful synergism between the automatic pipeline for multi-omics data processing of Genome Enhancer and the comprehensive bioinformatics toolbox of the geneXplain® platform integrated with TRANSFAC, TRANSPATH, and HumanPSD databases. With TRANSFAC full package you will be able to perform further processing of your analysis results received from Genome Enhancer, create, modify, and use already pre-defined workflows for your multi-omics data analysis, and work with data coming from other model organisms. For more info on TRANSFAC full package please refer to this table.









                                            

                                                                            
                                                           
                                                           

                                        
                        

                                                                        


   
    
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*), *.tsv


*.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 – exclusive access to Genome Enhancer or TRANSFAC full package including a wide range of tools and functionalities.








                                            

                                                                            
                                                           
                                                           

                                        
                        

                                                                        


   
    
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:



You are also very welcome to view or download the Genome Enhancer flyer.




                                            

                                                                            
                                                           
                                                           

                                        
                        

                                                                        


   
    
Videos

    


 




Below you will find a compilation of our videos referring to different aspects of Genome Enhancer.




In English Language










This video introduces you to the fully automated pipeline for the easy bioinformatics analysis of multi-omics data. (2:02 min)













This video shows how Genome Enhancer results can be interpreted for further use in clinic on the example of sensitivity prediction towards VEGFA-targeted therapy for three colorectal cancer patients.  (5:51 min)





In Chinese Language










The video provides you with a preview to the user interface of Genome Enhancer, and shows how to perform an analysis using Genome Enhancer. (4:42 min)













This video uses transcriptomics data as an example to highlight the detailed content of the data analysis report obtained as result of an analysis by Genome Enhancer. (3:09 min)













Here, Genome Enhancer is applied to analyze multi-omics data of colorectal cancer cell lines to find master regulators and to predict drug compounds affecting them. Thereafter, the effect of the predicted drug compounds on tumors is verified in an animal experiment.







                                            

                                                                            
                                                           
                                                           

                                        
                        

                                                                        


   
    
References

    
    

  1. Lloyd, Katie, et al. “Using systems medicine to identify a therapeutic agent with potential for repurposing in Inflammatory Bowel Disease.” Disease models & mechanisms (2020).
    2. 

  2. Kel, Alexander, et al. “Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer.” BMC bioinformatics 20.4 (2019): 119.
    3. 

  3. 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.
    4. 

  4. 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.
    5. 

  5. 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.
    6. 



 


Disclaimer


The results of Genome Enhancer analysis, contained in any of the reports produced by this pipeline, are intended for research use only and should not be used for medical or professional advice. GeneXplain GmbH makes no guarantee of the comprehensiveness, reliability or accuracy of the information contained in the reports generated by Genome Enhancer.


Decisions regarding care and treatment of patients should be fully made by attending doctors. The predicted chemical compounds listed in the reports are given only for doctor’s consideration and they cannot be treated as prescribed medication. It is the physician’s responsibility to independently decide whether any, none or all of the predicted compounds can be used solely or in combination for patient treatment purposes, taking into account all applicable information regarding FDA prescribing recommendations for any therapeutic and the patient’s condition, including, but not limited to, the patient’s and family’s medical history, physical examinations, information from various diagnostic tests, and patient preferences in accordance with the current standard of care. Whether or not a particular patient will benefit from a selected therapy is based on many factors and can vary significantly.


The compounds predicted to be active against the identified drug targets in the reports are not guaranteed to be active against any particular patient’s condition. GeneXplain GmbH does not give any assurances or guarantees regarding the treatment information and conclusions given in the reports. There is no guarantee that any third party will provide a refund for any of the treatment decisions made based on these results. None of the listed compounds was checked by Genome Enhancer for adverse side-effects or even toxic effects.


The analysis reports contain information about chemical drug compounds, clinical trials and disease biomarkers retrieved from the HumanPSD™ database of gene-disease assignments maintained and exclusively distributed worldwide by geneXplain GmbH. The information contained in this database is collected from scientific literature and public clinical trials resources. It is updated to the best of geneXplain’s knowledge however we do not guarantee completeness and reliability of this information leaving the final checkup and consideration of the predicted therapies to the medical doctor. In all cases, the end user (including researchers and medical doctors) accepts full responsibility for all risks associated with using of information, contained in the reports generated by Genome Enhancer.


The scientific analysis underlying the Genome Enhancer reports employs a complex analysis pipeline which uses geneXplain’s proprietary Upstream Analysis approach, integrated with TRANSFAC® and TRANSPATH® databases maintained and exclusively distributed worldwide by geneXplain GmbH. The pipeline and the databases are updated to the best of geneXplain’s knowledge and belief, however, geneXplain GmbH shall not give a warranty as to the characteristics or to the content and any of the results produced by Genome Enhancer. Moreover, any warranty concerning the completeness, up-to-dateness, correctness and usability of Genome Enhancer information and results produced by it, shall be excluded.


The results produced by Genome Enhancer, including the analysis reports, severely depend on the quality of input data used for the analysis. It is the responsibility of Genome Enhancer users to check the input data quality and parameters used for running the Genome Enhancer pipeline.


Note that the text given in the reports is not unique and can be fully or partially repeated in other Genome Enhancer analysis reports, including reports of other users. This should be considered when publishing any results or excerpts from the reports. This restriction refers only to the general description of analysis methods used for generating the reports. All data and graphics referring to the concrete set of input data, including lists of mutated genes, differentially expressed genes/proteins/metabolites, functional classifications, identified transcription factors and master regulators, constructed molecular networks, lists of chemical compounds and reconstructed model of molecular mechanisms of the studied pathology are unique in respect to the used input data set and Genome Enhancer pipeline parameters used for the current run.




                                            

                                                                            
                                                           
                                                           

                                 

    
    

    


                       
                 

                     
                         


                                     
                        

                            
                    
                

    






    

    
 

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