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Upstream analysis

Discover unanticipated causal relationships in your data with our unique upstream analysis.

The geneXplain platform

A versatile online toolbox for bioinformatics, systems biology and cheminformatics


The Gold Standard: more than 6500 positional weight matrices, and more than 30 million sites from high-throughput approaches!


Predict activity spectra of substances, and exploredrug-drug interactions and relationships between biological activities with PASS, GUSAR and PharmaExpert.

Special offer

During these challenging times geneXplain would like to support you to the best of our ability. From March 24 to April 30 we offer discounts on our software products and databases for the needs of biomedical research. You will find the full offer description here. We wish all of you to stay safe and healthy.

Precision medicine

Keeping our key goal on drug target identification, our analysis methods allow finding of currently activated targets in the examined patient data and selection of the best fit therapy for every studied case.


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Genome Enhancer is a fully automated pipeline for patient’s multi-omics data analysis. It generates a comprehensive 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. Genome Enhancer is using TRANSFAC®, TRANSPATH® and HumanPSD™ databases for the performed analysis. Learn more about Genome Enhancer.


Integrated promoter and pathway (“upstream”) analysis lays at the core of our approach to analyzing changes in gene or protein signatures in a cell as a consequence, for example, of disease pathogenesis. To reveal the full power of the platform and the upstream analysis, we recommend to apply it together with the databases TRANSFAC® and TRANSPATH®.


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The geneXplain platform is designed to ease the life of the bioinformatics expert who is in charge to evaluate experimental high-throughput data, but also effectively supports the experimental researcher to interpret his/her valuable data with an intuitive user interface. You are cordially invited to learn more about the geneXplain platform.

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The gold standard in the field of transcriptional regulation. This database comprises a unique collection of information about transcription factors (TFs), their genomic binding sites and binding site models (positional weight matrices), suitable for search for new TF binding sites. Learn more about the TRANSFAC database.

Systems biology

It is our wish to contribute to state of the art systems biological research by offering a comprehensive view of molecular and genetic networks operating in and constituting human cells.


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In addition to the TRANSPATH database (see above), we make available the world’s largest collection of interactions and pathways, the GeneWays database, through our geneXplain platform.
HumanPSD Logo
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The Human Proteome Survey Database (HumanPSD) is a rich compendium of human, mouse and rat proteins, their disease associations, biomarker properties and drug associations.

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The most comprehensive information repository on enzymes and enzyme ligand data. BRENDA is an indispensable resource when working with metabolic networks.


As soon as a potential target has been identified, for instance with our proprietary upstream analysis approach, the next question will be about drugs that may bind to that target. To adress this and related problems, we incorporated several stand-alone cheminformatics tools in our product range.

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Based on the world’s largest data collections pertaining to the biological activities of chemical compounds and their structures, PASS and PharmaExpert enable users to identify potential lead structures out of millions of chemical substances, thereby efficiently shortening development times for specific drugs or molecular probes for research purposes.

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PharmaExpert analyzes the relationships between biological activities, drug-drug interactions and multiple targeting of chemical compounds and selects compounds that have a pre-defined biological activity. It helps answer a question like “How to select the most promising compounds among those known to interact with the selected protein?

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Particularly valuable for experts is the program GUSAR, which enables construction of highly specific models based on own data sets.


Find history in our archive.
April 2, 2020

GeneXplain will be holding a free webinar “COVID-19 – online discovery of prospective drug targets and treatments with Genome Enhancer” on 7th and 14th of April. Register here for a convenient time for your time zone.

February 25, 2020

Join us for the Molecular Med TRI-CON 2020 in San Francisco on 1-4 March. We will be glad to meet you at our booth #524.

January 22, 2020

The video record of the passed webinar on omics data analysis and modeling organized by Optogenerapy EU project and geneXplain GmbH is available on our YouTube channel.

January 16, 2020

GeneXplain announces:

TRANSFAC® 2020.1
HumanPSDTM 2020.1

January 14, 2020

We are pleased to invite you to a free webinar “Omics data analysis and modelling using Genome Enhancer and its application to Optogenerapy project” organized jointly by geneXplain GmbH and Optogenerapy project EU, which will be held on January 21st, 2020 at 3 PM CET. Register here to join.