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Understanding and reconstructing biological pathways

General info

Date from - to
05 Apr 2005 - 05 Jun 2011
Project leader(s)
Moerland, Perry D. Dr. ir.
Evelo, Chris T.A. Dr. ir.
Prof. dr. Rogier Versteeg
Prof. dr. Peter A.J. Hilbers
Kampen, van Antoine Prof. dr.


DNA microarrays are used to elucidate biological pathways. To visualize the expression data in a pathway context, the data can be linked to a pathway database (e.g., KEGG or GenMapp). These data can give even more insights in the biological processes if more advanced and sophisticated databases and tools would be available. The development of such pathway databases, as well as a more effective integration with analysis and visualization tools, is the focus of this project. To this end, a knowledge base for the (semi-)automatic interpretation of microarray data in the context of biological pathways has been developed. This knowledge base uses pathway databases and an ontology-based representation of the data, and adds domain knowledge that helps biologists to fully understand his data. Integration of other types of data will aid further understanding, as well as reconstruction, of biological pathways. New methodologies may identify missing genes in pathways and may reconstruct larger parts of the pathways. The project uses graph-based representation of time-series data to progressively unravel regulatory pathways. Also, ranking methods and kernel-based methods are used to integrate microarray data with other types of genomics data to unravel networks.

Link to the end report of this project


  • The Emerging World of Wikis
  • WikiPathways: Pathway Editing for the People
  • The role of bioinformatics in pathway curation
  • The NuGO proof of principle study package: a collaborative research effort of the European Nutrigenomics Organisation
  • Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways
  • Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases
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