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.


Integrated promoter and pathway (“upstream”) analysis lies 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®.

Learn more
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.

Learn more
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.
Learn more
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
Learn more
The Human Proteome Survey Database (HumanPSD) is a rich compendium of human, mouse and rat proteins, their disease associations, biomarker properties and drug associations.

Learn more
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.

Learn more
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.

Learn more
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?

Learn more
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.

March 13-15, 2018

GeneXplain will participate in the Human Genome Meeting (HGM) 2018 in Yokohama, Japan. We have a joint booth with Kazusa Genome Technologies, KGT, a distributor of our products.
Read more about HGM2018

March, 2018

Korean scientists interested in our cancer software, please contact our distributor 3BIGS for more information.


February 12-14, 2018


Genexplain’s CSO Alexander Kel participate in the workshop on Gene Regulation in Ljubljana. Main topic of the workshop will be ‘Representing and Assessing Transcription Factor Binding Specificity’ (RATFBS).

Workshop link

30 years TRANSFAC


GeneXplain will sponsor the workshop on “Bioinformatics of Gene Regulation” according to the 30th birthday of TRANSFAC® database (March 7-9, in Göttingen).

Registration is free!

Read more

January 15, 2018

GeneXplain announces:

TRANSFAC® 2018.1
HumanPSDTM 2018.1