geneXplain - GeneXplain provides bioinformatics, systems biology and cheminformatics software and databases for life science and medical research.

TRANSFAC 2.0 is available in various packages

The TRANSFAC 2.0 comprehensively addresses the syntax and semantics of gene regulation: explore the genomic language that orchestrates the activation patterns of genes with it.
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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 cancerneurodegenerative diseasesinfectious diseasesdiabetes and metabolic diseaseshypertension. Genome Enhancer is using TRANSFAC®, TRANSPATH® and HumanPSD™ databases for the performed analysis. Learn more about Genome Enhancer.

Machine Learning and Artificial Intelligence

GeneXplain predicts genomic transcription factor (TF) binding sites and composite regulatory regions using such algorithms of Machine Learning (ML) and Artificial Intelligence (AI) as Genetic Algorithms and Sparse Logistic Regression.

TFBS combinatorial analysis with AI and ML

Predict TF binding sites in tissue/cell type/induction-specific combinatorial context. Search for specific TF binding regions in your sequence by scanning it through the TRANSFAC® library with over 100.000 MEALR models (Motif Enrichment Analysis by Logistic Regression). Learn more >>

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Identify combinations of
TF binding sites that are overrepresented in the regulatory sequences under study compared to a background set of sequences using our in-house implementation of a genetic algorithm called Composite Module Analyst (CMA). Learn more>>


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.


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Upcoming events
August 20, 2024

ATAC-seq and enhancers free webinar

The next Coffee break with TRANSFAC will be held on August 20th at 10 AM CEST. Leave your question for the upcoming event or receive event joining link to your email address. See you soon!

July 9, 2024

Release 2024.1

The next Coffee break with TRANSFAC will be held on July 9th at 10 AM CEST. Leave your question for the upcoming event or receive event joining link to your email address. See you soon!

July 4, 2024

geneXplain release 2024.1

New release of the geneXplain products – check all new features here!

June 18-21, 2024

GlioResolve consortium meeting and training is coming up. GeneXplain will give two lectures: (1) ML and AI in cancer research and (2) From DNA motifs to networks and drug targets. Check out how this project is developing the new TME-targeting precision medicine platform aiming to build the basis for fighting such complicated pathology as glioblastoma.