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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.

TRANSFAC 2.0 to be launched in summer 2021

The TRANSFAC 2.0 will comprehensively address the syntax and semantics of gene regulation: with it you will be able to explore the genomic language that orchestrates the activation patterns of genes. Follow the news on TRANSFAC 2.0 page.

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. Proven applications include cancer, neurodegenerative diseases, infectious diseases, diabetes and metabolic diseases. 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.
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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.
July 06, 2021

New releases of PASS and PharmaExpert, PASS 2020 and PharmaExpert 2020, respectively, are available now. Find out about new features in PASS and PharmaExpert.

June 1, 2021

Check out a recent publication applying TRANSFAC®, TRANSPATH® and geneXplain platform for studying of mechanisms by which MyD88/TLR signaling enhances clearance of Borrelia burgdorferi by macrophages. Link to full text.

May 19, 2021

Join us for a free webseminar “A computationally aided strategy to recover gene activity profiles from post-mortem HIV+ brain specimens” on May 19th at 6 PM CEST. To receive the webseminar joining link, please register here.

March 17, 2021

Our new publication ‘Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer’, which was released in the scope of the MyPathSem project, is now out! Full text can be found here.

March 15, 2021


TRANSFAC 2.0 to be released in summer 2021!

Explore the syntax and semantics of gene regulation with this next generation tool.

You will find more details here.