A data integration platform for generating patient-specific signaling pathways for personalized treatment decisions in clinical applications

Eine Datenintegrationsplattform für die Generierung von Patienten-spezifischen Signalwegen für individualisierte Behandlungsentscheidungen in klinischen Anwendungen

A collaborative project funded by the German Federal Ministry of Education and Research (BMBF) in the funding program
“i:DSem – Integrative Datensemantik in der Systemmedizin

Molecular biomarkers play a role in the diagnosis of cancer. Individualized treatment decisions and specialized drugs warrant the need to broaden the focus from singular biomarkers to pathways. While Omics technologies allow the parallel measurement of many different markers, pathway databases offer vast amounts of knowledge on biological networks. The aim of the MyPathSem project is to present the most relevant, meaningful and interpretable patient-specific pathways to clinicians and researchers. More specifically:

  • to link clinical information systems with patient-specific Omics data;
  • to generate a tool for data integration and easy access in a clinical environment;
  • to collect information from public pathway and literature databases;
  • to develop methods to generate context-specific pathways from individual patient data;
  • to apply the new tools on data from colorectal and metastatic cancer;
  • to test the utility in a clinical research setting; to integrate the tools into the geneXplain platform to make it available to a broader community; and, thus, to reduce the gap between patient centered routine documentation and ontology-driven pathway and gene annotation and establish a seamless data-flow from single patient data to Systems Medicine.

It is geneXplain’s task to contribute a user-friendly computer platform and to provide a prototypic version of an integrated toolbox that can be disseminated among research clinicians for systematic and large-scale validation of the project achievements. GeneXplain will also help disseminating the toolbox through its commercial channels, thereby contributing to the required sustainability of the project.

Link to project page with further info.


Wingender, E., Schoeps, T., Haubrock, M., Krull, M. and Dönitz, J. (2018) TFClass: expanding the classification of human transcription factors to their mammalian orthologs. Nucleic Acids Res. 46, D343-D347. doi: 10.1093/nar/gkx987.  Link

Stegmaier, P., Kel, A and Wingender, E. (2017) geneXplainR: An R interface for the geneXplain platform. J. Open Source Softw. 2, 412. doi: 10.21105/joss.00412. Link

Further information

Project page of BMBF (in German)
Project page of the Institute of Bioinformatics at UMG

Contract no.

031L0024 B

Contract period

March 1st, 2016 – February 28th, 2019


The project is coordinated by Prof. Dr. Tim Beissbarth and Dr. Frank Kramer, Institute of Medical Statistics, University Medical Center Göttingen (UMG), Germany.

The consortium consists of 6 partners, 5 of them belonging to UMG, the sixth is geneXplain in Wolfenbüttel.